Humanized anti-egfl7 antibodies and methods using same

ABSTRACT

The present invention concerns antibodies to EGFL7 and the uses of same.

RELATED APPLICATION

This application is a divisional of U.S. application Ser. No.12/776,259, filed 7 May 2010, which claims priority under 35 USC 119(e)to provisional application No. 61/176,817, filed 8 May 2009, thecontents of which are incorporated herein by reference.

FIELD OF THE INVENTION

The present invention relates generally to the field of molecularbiology. More specifically, the invention concerns anti-EGFL7antibodies, and uses of same.

BACKGROUND OF THE INVENTION

The development of a vascular supply is a fundamental requirement formany physiological and pathological processes. Actively growing tissuessuch as embryos and tumors require adequate blood supply. They satisfythis need by producing pro-angiogenic factors, which promote new bloodvessel formation from existing vessels via a process calledangiogenesis; or from progenitor cells through a process calledvasculogenesis. Tubulogenesis is an essential step in vasculardevelopment. Vascular tube formation is a complex but orderly biologicalevent involving all or many of the following steps: a) endothelial cells(EC) proliferate from existing ECs or differentiate from progenitorcells; b) EC migration; c) ECs coalesce to form cord-like structures; d)vascular cords then undergo tubulogenesis to form vessels with a centrallumen e) existing cords or vessels send out sprouts to form secondaryvessels (angiogenesis); f) primitive vascular plexus undergo furtherremodeling and reshaping; and g) peri-endothelial cells are recruited toencase the endothelial tubes, providing maintenance and modulatoryfunctions to the vessels; such cells including pericytes for smallcapillaries, smooth muscle cells for larger vessels, and myocardialcells in the heart. Hanahan, D. Science 277, 48-50 (1997); Hogan, B. L.& Kolodziej, P. A. Nature Reviews Genetics. 3, 513-23 (2002); Lubarsky,B. & Krasnow, M. A. Cell. 112, 19-28 (2003).

It is now well established that angiogenesis, which involves theformation of new blood vessels from preexisting endothelium, isimplicated in the pathogenesis of a variety of disorders. These includesolid tumors and metastasis, atherosclerosis, retrolental fibroplasia,hemangiomas, chronic inflammation, intraocular neovascular syndromessuch as proliferative retinopathies, e.g., diabetic retinopathy,age-related macular degeneration (AMD), neovascular glaucoma, immunerejection of transplanted corneal tissue and other tissues, rheumatoidarthritis, and psoriasis. Folkman et al., J. Biol. Chem., 267:10931-10934 (1992); Klagsbrun et al., Annu. Rev. Physiol., 53: 217-239(1991); and Garner A., “Vascular diseases”, In: Pathobiology of OcularDisease. A Dynamic Approach, Garner A., Klintworth G K, eds., 2ndEdition (Marcel Dekker, NY, 1994), pp 1625-1710.

In the case of tumor growth, angiogenesis appears to be crucial for thetransition from hyperplasia to neoplasia, and for providing nourishmentfor the growth and metastasis of the tumor. Folkman et al., Nature, 339:58 (1989). The neovascularization allows the tumor cells to acquire agrowth advantage and proliferative autonomy compared to normal cells. Atumor usually begins as a single aberrant cell which can proliferateonly to a size of a few cubic millimeters due to the distance fromavailable capillary beds, and it can stay ‘dormant’ without furthergrowth and dissemination for a long period of time. Some tumor cellsthen switch to the angiogenic phenotype to activate endothelial cells,which proliferate and mature into new capillary blood vessels. Thesenewly formed blood vessels not only allow for continued growth of theprimary tumor, but also for the dissemination and recolonization ofmetastatic tumor cells. Accordingly, a correlation has been observedbetween density of microvessels in tumor sections and patient survivalin breast cancer as well as in several other tumors. Weidner et al., N.Engl. J. Med, 324: 1-6 (1991); Horak et al., Lancet, 340: 1120-1124(1992); Macchiarini et al., Lancet, 340: 145-146 (1992). The precisemechanisms that control the angiogenic switch is not well understood,but it is believed that neovascularization of tumor mass results fromthe net balance of a multitude of angiogenesis stimulators andinhibitors (Folkman, 1995, Nat Med 1(1):27-31).

The process of vascular development is tightly regulated. To date, asignificant number of molecules, mostly secreted factors produced bysurrounding cells, have been shown to regulate EC differentiation,proliferation, migration and coalescence into cord-like structures. Forexample, vascular endothelial growth factor (VEGF) has been identifiedas the key factor involved in stimulating angiogenesis and in inducingvascular permeability. Ferrara et al., Endocr. Rev., 18: 4-25 (1997).The finding that the loss of even a single VEGF allele results inembryonic lethality points to an irreplaceable role played by thisfactor in the development and differentiation of the vascular system.Furthermore, VEGF has been shown to be a key mediator ofneovascularization associated with tumors and intraocular disorders.Ferrara et al., Endocr. Rev., supra. The VEGF mRNA is overexpressed bythe majority of human tumors examined. Berkman et al., J. Clin. Invest.,91: 153-159 (1993); Brown et al., Human Pathol., 26: 86-91 (1995); Brownet al., Cancer Res., 53: 4727-4735 (1993); Mattern et al., Brit. J.Cancer, 73: 931-934 (1996); Dvorak et al., Am. J. Pathol., 146:1029-1039 (1995).

Some of the steps during vessel tube formation are still poorly defined.Particularly, little is know about how tubulogenesis is regulated—howvascular cords progress to become tubes, and what factors regulate thistransition. In view of the role of vasculogenesis and angiogenesis inmany diseases and disorders, it is desirable to have a means of reducingor inhibiting one or more of the biological effects causing theseprocesses. All references cited herein, including patent applicationsand publications, are incorporated by reference in their entirety.

SUMMARY OF THE INVENTION

The invention is in part based on a variety of antibodies to EGFL7.EGFL7 presents as an important and advantageous therapeutic target, andthe invention provides antibodies as therapeutic and diagnostic agentsfor use in targeting pathological conditions associated with expressionand/or activity of EGFL7. Accordingly, the invention provides methods,compositions, kits and articles of manufacture related to EGFL7.

For example, in some embodiments, the invention provides anti-EGFL7antibodies. In some embodiments, the invention provides an anti-EGFL7antibody comprising a variable domain comprising at least one, two,three, four or five hypervariable region (HVR) sequences selected fromthe group consisting of: (i) HVR-L1 comprising KX₁SX₂SX₃DYX₄GDSYX₅S,wherein X₁ is A or R; X₂ is H or Q; X₃ is G or V; X₄ is selected fromthe group consisting of D, L, R, S, and W; and X₅ is M or V (SEQ ID NO:210); (ii) HVR-L2 comprising GASX₁X₂EX₃, wherein X₁ is N or Y; X₂ isselected from the group consisting of L, R and Y; and X₃ is Q or S (SEQID NO: 211); (iii) HVR-L3 comprising QQNNEX₁PX₂T, wherein X₁ is D or E;and X₂ is F or Y (SEQ ID NO: 212); (iv) HVR-H1 comprisingGX₁X₂X₃X₄TYGX₅S, wherein X₁ is H or V; X₂ is R or T; X₃ is selected fromthe group consisting of F, G, R, and S; X₄ is selected from the groupconsisting of D, G, R, and T; and X₅ is M or Y (SEQ ID NO: 213); (v)HVR-H2 comprising GWINX₁X₂SGVPTX₃AX₄X₅X₆X₇X₈, wherein X₁ is selectedfrom the group consisting of I, M, T, and W; X₂ is H or R; X₃ isselected from group consisting of I, M, T, and Y; X₄ is D or H; X₅ isselected from group consisting of D, M and T; X₆ is F or Y; X₇ is K orS; and X₈ is G or R (SEQ ID NO: 214, and (vi) HVR-H3 comprisingAX₁LGSX₂AVDX₃, wherein X₁ is N or R; X₂ is selected from the groupconsisting of C, S, and Y; and X₃ is A or Y (SEQ ID NO: 215). In someembodiments, the anti-EGFL7 antibody comprises all six of theaforementioned HVRs. In some embodiments, HVR-L1 comprises an amino acidsequence selected from SEQ ID NOs: 31 and 37-43, HVR-L2 comprises anamino acid sequence selected from the group consisting of SEQ ID NOs: 32and 44-47, HVR-L3 comprises an amino acid sequence selected from thegroup consisting of SEQ ID NOs: 33 and 48, HVR-H1 comprises an aminoacid sequence selected from the group consisting of SEQ ID NOs: 34 and49-57, HVR-H2 comprises an amino acid sequence selected from the groupconsisting of SEQ ID NOs: 35 and 58-73, and HVR-H3 comprises an aminoacid sequence selected from the group consisting of SEQ ID NOs: 36 and74-77. In some embodiments the heavy chain comprises the followingframework sequences: FR-H1 comprises EX₁QLVESGGGLVQPGGSLRLSCAAS, whereinX₁ is I or V (SEQ ID NO: 216); FR-H2 comprises WVRQAPGKGLEWX₁, whereinX₁ is I or V (SEQ ID NO: 217); FR-H3 comprisesRFTX₁SX₂DX₃SX₄X₅TX₆YLQMNSLRAEDTAVYX₇CAR, wherein X₁ is F or I; X₂ is Lor R; X₃ is N or T, X₄ is selected from the group consisting of A, E, Kand T; X₅ is N or S; X₆ is selected from the group consisting of A, L,M, T and V; and X₇ is F or Y (SEQ ID NO: 218); and FR-H4 comprisesWGQGTLVTVSS (SEQ ID NO: 219). In some embodiments, the heavy chaincomprises the following framework sequences: FR-H1 comprisesEVQLVESGGGLVQPGGSLRLSCAAS (SEQ ID NO: 197); FR-H2 comprisesWVRQAPGKGLEWV (SEQ ID NO: 198); FR-H3 comprisesRFTISX₁DNSKNTX₂YLQMNSLRAEDTAVYYCAR, wherein X₁ L or R; X₂ is selectedfrom the group consisting of A, L, M, T and V (SEQ ID NO: 220); andFR-H4 comprises WGQGTLVTVSS (SEQ ID NO: 200). In some embodiments, thelight chain comprises the following framework sequences: FR-L1 comprisesDIQMTQSPSSLSASVGDRVTITC (SEQ ID NO: 201), FR-L2 comprisesWYQQKPGKAPKLLIY (SEQ ID NO: 202), FR-L3 comprisesGVPSRFSGSGSGTDFTLTISSLQPEDFATYYC (SEQ ID NO: 203), FR-L4 comprisesFGQGTKVEIK (SEQ ID NO: 221) or FGQGTKVEIKR (SEQ ID NO: 204). In someembodiments, the light chain comprises the variable domain sequence of4F11.v17 or 4F11.v22 as shown in FIG. 15 (SEQ ID NOs: 82 and 83). Insome embodiments, the heavy chain comprises the variable domain sequenceof 4F11.v17 or 4F11.v22 as shown in FIG. 16 (SEQ ID NOs: 84 and 85). Insome embodiments, the invention provides an antibody wherein the lightchain comprises the variable domain sequence of 4F11.v17 as shown inFIG. 15 (SEQ ID NO: 82) and the heavy chain comprises the variabledomain sequence of 4F11.v17 as shown in FIG. 16 (SEQ ID NO: 84). In someembodiments, the invention provides an antibody wherein the light chaincomprises the variable domain sequence of 4F11.v22 as shown in FIG. 15(SEQ ID NO: 83) and the heavy chain comprises the variable domainsequence of 4F11.v22 as shown in FIG. 16 (SEQ ID NO: 85).

In some embodiments, the invention provides a anti-EGFL7 antibodycomprising a variable domain comprising at least one, two, three, fouror five HVR sequences selected from the group consisting of: (i) HVR-L1comprising X₁X₂X₃X₄X₅X₆VX₇X₈X₉X₁₀ITYLX₁₁, wherein X₁ is selected fromthe group consisting of L, Q, R, S, and T; X₂ is selected from the groupconsisting of P, T, and W; X₃ is H or S; X₄ is D or Q; X₅ is G or S; X₆is L or V; X₇ is H or P; X₈ is selected from the group consisting of I,L, P, T, and Y; X₉ is selected from the group consisting of N, Q or S;X₁₀ is selected from the group consisting of A, G, and S; and X₁₁ is Gor H (SEQ ID NO: 222); (ii) HVR-L2 comprising RVSNX₁X₂S, wherein X₁ is Dor R; and X₂ is selected from the group consisting of A, G, F, I, and T(SEQ ID NO: 223); (iii) HVR-L3 comprising X₁QSX₂X₃VPLT, wherein X₁ isselected from the group consisting of A, G, I, K, L, N, S, T, and V; X₂is C or T; and X₃ is F or H (SEQ ID NO: 224); (iv) HVR-H1 comprisingGYX₁X₂X₃DX₄YX₅N, wherein X₁ is N or T; X₂ is F or V; X₃ is selected fromthe group consisting of I, M, R, and S; X₄ is selected from the groupconsisting of Y, Q, and K; and X₅ is I or M (SEQ ID NO: 225); (v) HVR-H2comprising GDINX₁X₂X₃X₄X₅X₆HX₇X₈X₉X₁₀X₁₁X₁₂X₁₃, wherein X₁ is selectedfrom the group consisting of A, L, N, and P; X₂ is selected from thegroup consisting of D, L, and R; X₃ is selected from the groupconsisting of G, K, N, R, S, and Y; X₄ is G or S; X₅ is selected fromthe group consisting of G, I, K, R, S, T, and V; X₆ is selected from thegroup consisting of G, R, and T; X₇ is selected from the groupconsisting of I, V, and Y; X₈ is N or S; X₉ is selected from the groupconsisting of A, N, and Q; X₁₀ is K or V; X₁₁ is F or Q; X₁₂ is K or T;and X₁₃ is selected from the group consisting of G, H, R, and S (SEQ IDNO: 226), and (vi) HVR-H3 comprising X₁REGVYHX₂YDDYAX₃DY, wherein X₁ isselected from the group consisting of A, N, and T; X₂ is D or P; and X₃is M or W (SEQ ID NO: 227). In some embodiments, the anti-EGFL7 antibodycomprises all six of the aforementioned HVRs. In some embodiments,HVR-L1 comprises an amino acid sequence selected from SEQ ID NOs: 100and 106-124, HVR-L2 comprises an amino acid sequence selected from thegroup consisting of SEQ ID NOs: 101 and 125-129, HVR-L3 comprises anamino acid sequence selected from the group consisting of SEQ ID NOs:102 and 130-145, HVR-H1 comprises an amino acid sequence selected fromthe group consisting of SEQ ID NOs: 103 and 146-153, HVR-H2 comprises anamino acid sequence selected from the group consisting of SEQ ID NOs:104 and 154-187, and HVR-H3 comprises an amino acid sequence selectedfrom the group consisting of SEQ ID NOs: 105 and 188-192. In someembodiments, the heavy chain comprises the following frameworksequences: FR-H1 comprises EVQLVESGGGLVQPGGSLRLSCAAS (SEQ ID NO: 197);FR-H2 comprises WVRQAPGKGLEWX₁, wherein X₁ is I or V (SEQ ID NO: 228);FR-H3 comprises RX₁TX₂SX₃DX₄SX₅X₆TX₇YX₈QMNSLRAEDTAVYYC, wherein X₁ is For V; X₂ is I or L; X₃ is selected from the group consisting of L, R,and V; X₄ is K or N; X₅ is selected from the group consisting of K, N,R, and S; X₆ is N or S; X₇ is selected from the group consisting of A,L, and V; and X₈ is L or M (SEQ ID NO: 229); and FR-H4 comprisesWGQGTLVTVSS (SEQ ID NO: 200). In some embodiments, the heavy chaincomprises the following framework sequences: FR-H1 comprisesEVQLVESGGGLVQPGGSLRLSCAAS (SEQ ID NO: 197); FR-H2 comprisesWVRQAPGKGLEWV (SEQ ID NO: 198); FR-H3 comprisesRFTISRDX₁SKNTX₂YLQMNSLRAEDTAVYYCAR, wherein X₁ is N or K; and X₂ isselected from the group consisting of A, L, and V (SEQ ID NO: 230); andFR-H4 comprises WGQGTLVTVSS (SEQ ID NO: 200). In some embodiments, thelight chain comprises the following framework sequences: FR-L1 comprisesDIQMTQSPSSLSASVGDRVTITC (SEQ ID NO: 201), FR-L2 comprisesWYQQKPGKAPKLLIY (SEQ ID NO: 202), FR-L3 comprisesGVPSRFSGSGSGTDFTLTISSLQPEDFATYYC (SEQ ID NO: 203), FR-L4 comprisesFGQGTKVEIK (SEQ ID NO: 221) or FGQGTKVEIKR (SEQ ID NO: 204). In someembodiments, the light chain comprises the variable domain sequence of18F7.v6 or 18F7.v6k as shown in FIG. 27 (SEQ ID NOs: 193 and 194). Insome embodiments, the heavy chain comprises the variable domain sequenceof 18F7.v6 or 18F7v6k as shown in FIG. 28 (SEQ ID NOs: 195 and 196). Insome embodiments, the invention provides an antibody wherein the lightchain comprises the variable domain sequence of 18F7.v6 as shown in FIG.27 (SEQ ID NO: 193) and the heavy chain comprises the variable domainsequence of 18F7.v6 as shown in FIG. 28 (SEQ ID NO: 195). In someembodiments, the invention provides an antibody wherein the light chaincomprises the variable domain sequence of 18F7.v6k as shown in FIG. 27(SEQ ID NO: 194) and the heavy chain comprises the variable domainsequence of 18F7.v6k as shown in FIG. 28 (SEQ ID NO: 196).

In some embodiments, the invention provides an antibody where at least aportion of the framework sequence is a human consensus frameworksequence. In some embodiments, the antibody comprises human κ subgroup 1consensus framework sequence. In some embodiments, the antibodycomprises heavy chain human subgroup III consensus framework sequence.

In some embodiments, the invention provides an anti-EGFL7 antibody thatis a bispecific antibody. In some embodiments, the bispecific antibodybinds to vascular endothelial growth factor (VEGF), e.g. to the sameVEGF epitope as bevacizumab or ranibizumab.

In some embodiments, the invention provides a nucleic acid encoding anantibody of the invention. In some embodiments, the invention provides avector comprising such a nucleic acid. In some embodiments, theinvention provides a host cell comprising the nucleic acid or vector.

In some embodiments, the invention provides a composition comprising anantibody of the invention. In some embodiments, the compositioncomprises a carrier. In some embodiments, the composition in apharmaceutical composition.

In some embodiments, the invention provides a method for making ananti-EGFL7 antibody by expressing in a suitable host cell a vectorcomprising a nucleic acid encoding an antibody of the invention andrecovering the antibody. In some embodiments, the host cell isprokaryotic. In some embodiments, the host cell is eukaryotic.

In some embodiments, the invention provides a method for treating atumor, a cancer, or a cell proliferative disorder, the method comprisingadministering an effective amount of an anti-EGFL7 antibody of theinvention to an individual in need of such treatment. In someembodiments, the invention provides an anti-EGFL7 antibody for use inthe treatment of a tumor, a cancer, or a cell proliferative disorder. Insome embodiments, the cancer is selected from the group consisting ofbreast cancer, colorectal cancer, lung cancer, esophageal cancer,bladder cancer, ovarian cancer, pancreatic cancer, and hepatocellularcarcinoma. In some embodiments, the cancer is breast cancer, colorectalcancer or lung cancer. In some embodiments, the cell proliferativedisorder is cancer.

In some embodiments, the treatment also comprises an effective amount ofa second medicament, wherein the anti-EGFL7 antibody is a firstmedicament. In some embodiments, the second medicament is anotherantibody, a chemotherapeutic agent, a cytotoxic agent, ananti-angiogenic agent, an immunosuppressive agent, a prodrug, acytokine, a cytokine antagonist, cytotoxic radiotherapy, acorticosteroid, an anti-emetic, a cancer vaccine, an analgesic, or agrowth-inhibitory agent. In some embodiments, the second medicament isan anti-VEGF antibody, e.g. bevacizumab. In some embodiments, the secondmedicament is administered prior to or subsequent to the administrationof the anti-EGFL7 antibody. In some embodiments, the second medicamentis administered concurrently with the anti-EGFL7 antibody.

In some embodiments, the invention provides a method of reducing orinhibiting angiogenesis in a subject having a pathological conditionassociated with angiogenesis, comprising administering to the subject anantibody of the invention, thereby reducing or inhibiting angiogenesisin the subject. In some embodiments, the invention provides an antibodyof the invention for use in the treatment of a pathological conditionassociated with angiogenesis. In some embodiments, the pathologicalcondition is a neoplastic condition. In some embodiments, thepathological condition in a non-neoplastic condition. In someembodiments, the non-neoplastic condition is selected from the groupconsisting of diabetic and other proliferative retinopathies,retinopathy of prematurity, neovascular glaucoma, age-related maculardegeneration, diabetic macular edema, corneal neovascularization,corneal graft neovascularization, retinal/choroidal neovascularization.

In some embodiments, the invention provides a method of enhancingefficacy of an anti-angiogenesis agent in a subject having apathological condition associated with angiogenesis, comprisingadministering to the subject an effective amount of an antibody of theinvention in combination with the anti-angiogenesis agent, therebyenhancing said anti-angiogenesis agent's inhibitory activity. In someembodiments, the invention provides an antibody of the invention for usein enhancing efficacy of an anti-angiogenesis agent in a subject havinga pathological condition associated with angiogenesis. In someembodiments, the pathological condition associated with angiogenesis isa tumor, cancer or cell proliferative disorder. In some embodiments, thepathological condition associated with angiogenesis in a non-neoplasticcondition. In some embodiments, the non-neoplastic condition is selectedfrom the group consisting of diabetic and other proliferativeretinopathies, retinopathy of prematurity, neovascular glaucoma,age-related macular degeneration, diabetic macular edema, cornealneovascularization, corneal graft neovascularization, retinal/choroidalneovascularization. In some embodiments, the anti-angiogenesis agent isadministered prior to or subsequent to the administration of theanti-EGFL7 antibody. In some embodiments, the anti-angiogenesis agent isadministered concurrently with the anti-EGFL7 antibody. In someembodiments, the anti-antigenesis agent is an anti-VEGF agent, ananti-VEGF antibody, e.g. bevacizumab or ranibizumab.

In some embodiments, the invention provides a method of reducing orinhibiting perfusion and permeability of a tumor in a subject,comprising administering to the subject an antibody of the invention. Insome embodiments, the invention provides an antibody of the inventionfor use in reducing or inhibiting perfusion and permeability of a tumorin a subject. In some embodiments, the method or use further comprisesadministering an anti-angiogenesis agent, e.g. an anti-VEGF agent (e.g.an anti-VEGF antibody such as bevacizumab.

BRIEF DESCRIPTION OF THE FIGURES

FIG. 1 depicts amino acid sequences of EGFL7 from mouse (SEQ ID NO: 1)and human (SEQ ID ON: 2). The locations of the EMI1, EMI2, EGF andcoiled-coiled domains are indicated. Truncated EGFL7 lacks thecoiled-coiled domains. The sequence of peptides EMI1 (SEQ ID NO: 3),EMI2 (SEQ ID NO: 4) and p2 (SEQ ID NO: 5), P4 (SEQ ID NO: 6), p5 (SEQ IDNO: 7), and p6 (SEQ ID NO: 8) are underlined.

FIG. 2 depicts the amino acid sequence of the variable light domain ofthe human Kappa I consensus (SEQ ID NO: 9) and 4F11.v1 (SEQ ID NO: 10).Positions are numbered according to Kabat and hypervariable regions areboxed.

FIG. 3 depicts the amino acid sequence of the variable heavy domain ofthe human subgroup III consensus (SEQ ID NO: 11) and 4F11.v1 (SEQ ID NO:12). Positions are numbered according to Kabat and hypervariable regionsare boxed.

FIG. 4 depicts oligonucleotides used to toggle positions in theFramework Toggle Library. The DNA sequence of 4F11.v1 and theoligonucleotides used to generate the framework toggle are shown. Theamino acid sequences of the original and some resulting framework toggleregions are also shown. In some cases additional amino acid residueswere also incorporated based on how the degenerate codons were designed.Sequence identifiers are shown in parentheses to the right of thecorresponding sequence (SEQ ID NOs: 13-28).

FIG. 5 depicts results demonstrating that mu4F11 binding to EGFL7 can beblocked by Peptide 2 (SEQ ID NO: 5), but not by overlapping Peptides 1or 3 (SEQ ID NOs: 29 and 30, respectively) or a random control peptide.

FIG. 6 depicts binding of phage displaying 4F11.v1 Fab to truncatedEGFL7 immobilized on a microtiter plate. Both samples of 4F11.v1 phageshow increased binding to immobilized EGFL7 as a function of increasingphage concentration. A control phage shows background binding similar tolevels of 4F11.v1 phage at low phage concentrations suggesting somenon-specific phage-EGFL7 interaction.

FIG. 7 depicts binding of phage displaying 4F11.v1 Fab to EMI2 domain orp2 peptide biotinylated either through a free amino or free thiol.

FIG. 8 depicts the abundance of residues found at each frameworkposition during the Framework Toggle. Amino acids introduced at eachframework position during the Framework Toggle are listed.

FIG. 9 depicts CDR sequence changes observed in each of the 6 “singleposition libraries” (SPLs) for each of the 3 frameworks. Libraries wereseparated by framework used (4F11.v1, 4F11.v2 and 4F11.v3). Changesobtained from each of the SPLs versus the particular CDR sequence arehighlighted. The VL and VH sequences outside of these changes wereidentical to the corresponding framework and are now shown. Sequenceidentifiers are shown in parentheses to the right of the correspondingsequence (SEQ ID NOs: 31-77). Individual sequences that appear more thanonce may not always have a corresponding sequence identifier.

FIG. 10 depicts the framework and library design for the variable lightdomain of limited libraries 1 and 2. The amino acid sequence of thehuman Kappa I consensus (SEQ ID NO: 9) and 4F11.v1 (SEQ ID NO: 10) areshown compared to the template used for library 1 (SEQ ID NO: 78) andlibrary 2 (SEQ ID NO: 79). Positions that were randomized to all 20amino acids are shown with slash through the amino acid.

FIG. 11 depicts the framework and library design for the variable heavydomain of limited libraries 1 and 2. The amino acid sequence of thehuman subgroup III consensus (SEQ ID NO: 11) and 4F11.v1 (SEQ ID NO: 12)are shown compared to the template used for library 1 (SEQ ID NO: 80)and library 2 (SEQ ID NO: 81). Positions that were randomized to all 20amino acids are shown with slash through the amino acid.

FIG. 12 depicts the frequency of changes observed at randomizedpositions in limited libraries 1 and 2. The preference of amino acidsselected at positions 53 and 54 in the light chain and 29, 52, and 98 inthe heavy chain is shown. The preference (Sigma) for any amino acid isreported as the number of standard deviations above a random chanceoccurrence of a given residue in the library assuming a binomialdistribution of amino acids. Scoring by this method accounts for theexpected codon bias and sampling statistics when establishing aconsensus.

FIGS. 13 & 14 depict inhibition of HUVEC adhesion to immobilized humanor mouse EGFL7 in vitro by humanized 4F11 variants. HUVECs (20,000cells/well) were allowed to adhere to 96 well plates coated with 5 μg/mlhuman or murine EGFL7 in the presence of increasing concentrations ofantibody. The number of cells that still adhered to the plates afterwashing were counted and calculated as percent of the total cells platedinto each well.

FIG. 15 depicts the amino acid sequence of the variable light domain ofthe human Kappa I consensus (SEQ ID NO: 9), 4F11.v1 (SEQ ID NO: 10),4F11.v17 (SEQ ID NO: 82), and 4F11.v22 (SEQ ID NO: 83). Positions arenumbered according to Kabat and hypervariable regions (SEQ ID NOs:234-236) are boxed.

FIG. 16 depicts the amino acid sequence of the variable heavy domain ofthe human subgroup III consensus (SEQ ID NO: 11), 4F11.v1 (SEQ ID NO:12), 4F11.v17 (SEQ ID NO: 84), and 4F11.v22 (SEQ ID NO: 85; SEQ ID NOs:238-240). Positions are numbered according to Kabat and hypervariableregions (SEQ ID NOs: 34, 35, 237) are boxed.

FIG. 17 depicts the amino acid sequence of the variable light domain ofthe human Kappa I consensus (SEQ ID NO: 9) and the 18F7-graft (SEQ IDNO: 86). Positions are numbered according to Kabat and hypervariableregions are boxed.

FIG. 18 depicts the amino acid sequence of the variable heavy domain ofthe human subgroup III consensus (SEQ ID NO: 11) and the 18F7-graft (SEQID NO: 87). Positions are numbered according to Kabat and hypervariableregions are boxed.

FIG. 19 depicts oligonucleotides used to toggle positions in theFramework Toggle Library. The DNA sequence of 18F7-graft and theoligonucleotides used to generate the framework toggle are shown. Theamino acid sequences of the original and some resulting framework toggleregions are also shown. In some cases additional amino acid residueswere also incorporated based on how the degenerate codons were designed.Sequence identifiers are shown in parentheses to the right of thecorresponding sequence (SEQ ID NOs: 88-99).

FIG. 20 depicts results demonstrating that mu18F7 binding to EGFL7 canbe blocked by EMI1 (SEQ ID NO: 3) or Peptide P5 (SEQ ID NO: 7), but notby Peptides P4 or P6 (SEQ ID NOs: 6 and 8, respectively). Chickenembryonic fibroblasts were transfected with a plasmid containing theHA-tagged full-length human EGFL7 cDNA. Cell lysate prepared fromtransfected cells was immunoprecipitated with mu18F7 in the presence of200-fold excess competitive peptides. Immunoprecipitates were analyzedby western blot using an anti-HA antibody.

FIG. 21 depicts binding of phage displaying 18F7-graft Fab to truncatedhuEGFL7 immobilized on a microtiter plate. Both samples of 18F7-graftphage show increased binding to immobilized EGFL7 as a function ofincreasing phage concentration. A control phage shows background bindingsimilar to levels of 18F7-graft phage at low phage concentrationssuggesting some non-specific phage-EGFL7 interaction.

FIG. 22 depicts binding of phage displaying 18F7-graft Fab to EMI1domain or p5 peptide biotinylated either through a free amino or freethiol.

FIG. 23 depicts the abundance of residues found at each frameworkposition during the Framework Toggle. Amino acids introduced at eachframework position during the Framework Toggle are listed.

FIG. 24 depicts CDR sequence changes observed in each of the 6 SPLs foreach of the 3 frameworks. Libraries were separated by framework used(18F7-graft, 18F7-K, 18F7-KV, and 18F7-KA). Changes obtained from eachof the SPLs versus the particular CDR sequence are highlighted. The VLand VH sequences outside of these changes were identical to thecorresponding framework and are now shown. Sequence identifiers areshown in parentheses to the right of the corresponding sequence (SEQ IDNOs: 100-192). Individual sequences that appear more than once may notalways have a corresponding sequence identifier.

FIG. 25 depicts inhibition of HUVEC adhesion to immobilized human ormouse EGFL7 in vitro by humanized 18F7 variants. HUVECs (20,000cells/well) were allowed to adhere to 96 well plates coated with 5 μg/mlhuman or murine EGFL7 in the presence of increasing concentrations ofantibody. The number of cells that still adhered to the plates afterwashing were counted and calculated as percent of the total cells platedinto each well.

FIG. 26 depicts inhibition of HUVEC transwell migration. HUVECs (50,000cells per well) were grown for 16 hours in the top chambers of transwellplates, and the membranes in the top chamber were coated with 5 μg/mlrecombinant human EGFL7 protein. Various concentrations of controlantibody (anti-IgE) or different variants of 18F7 were added to theculture medium in the top and bottom chambers, whereas 20 ng/ml ofrecombinant human VEGF-165 was added in the bottom wells to stimulateHUVEC migration. Cells migrated to the undersides of the top chamberswere counted and plotted against the treatments (antibodies andconcentrations).

FIG. 27 depicts the amino acid sequence of the variable light domain ofthe human Kappa I consensus (SEQ ID NO: 9), 18F7.v6 (SEQ ID NO: 193),and 18F7.v6k (SEQ ID NO: 194). Positions are numbered according to Kabatand hypervariable regions (SEQ ID NOs: 241, 101, 131) are boxed. Wheresequence for 18F7.v6k is not shown (in the second and third parts of thealignment), the corresponding sequence is identical to the sequence for18F7.v6.

FIG. 28 depicts the amino acid sequence of the variable heavy domain ofthe human subgroup III consensus (SEQ ID NO: 11), 18F7.v6 (SEQ ID NO:195), and 18F7.v6k (SEQ ID NO: 196). Positions are numbered according toKabat and hypervariable regions (SEQ ID NOs: 103, 242, 105) are boxed.Where sequence for 18F7.v6k is not shown (in the first and third partsof the alignment), the corresponding sequence is identical to thesequence for 18F7.v6.

FIG. 29 depicts inhibition of H1299 xenograft tumor growth usinghu18F7.v6k alone and in combination with an anti-VEGF antibody.

FIG. 30 depicts inhibition of LXFL 1674 xenograft tumor growth usinghu18F7.v6k alone and in combination with an anti-VEGF antibody.

FIG. 31 depicts inhibition of neonatal trachea vascularization usinghu18F7.v6k alone and in combination with an anti-VEGF antibody.

DETAILED DESCRIPTION OF THE INVENTION

The invention provides methods, compositions, kits and articles ofmanufacture for anti-EGFL7 antibodies.

Details of these methods, compositions, kits and articles of manufactureare provided herein.

General Techniques

The techniques and procedures described or referenced herein aregenerally well understood and commonly employed using conventionalmethodology by those skilled in the art, such as, for example, thewidely utilized methodologies described in Sambrook et al., MolecularCloning: A Laboratory Manual 3rd. edition (2001) Cold Spring HarborLaboratory Press, Cold Spring Harbor, N.Y. CURRENT PROTOCOLS INMOLECULAR BIOLOGY (F. M. Ausubel, et al. eds., (2003)); the seriesMETHODS IN ENZYMOLOGY (Academic Press, Inc.): PCR 2: A PRACTICALAPPROACH (M. J. MacPherson, B. D. Hames and G. R. Taylor eds. (1995)),Harlow and Lane, eds. (1988) ANTIBODIES, A LABORATORY MANUAL, and ANIMALCELL CULTURE (R. I. Freshney, ed. (1987)).

DEFINITIONS

An “isolated” antibody is one which has been identified and separatedand/or recovered from a component of its natural environment.Contaminant components of its natural environment are materials whichwould interfere with diagnostic or therapeutic uses for the antibody,and may include enzymes, hormones, and other proteinaceous ornonproteinaceous solutes. In preferred embodiments, the antibody will bepurified (1) to greater than 95% by weight of antibody as determined bythe Lowry method, and most preferably more than 99% by weight, (2) to adegree sufficient to obtain at least 15 residues of N-terminal orinternal amino acid sequence by use of a spinning cup sequenator, or (3)to homogeneity by SDS-PAGE under reducing or nonreducing conditionsusing Coomassie blue or, preferably, silver stain. Isolated antibodyincludes the antibody in situ within recombinant cells since at leastone component of the antibody's natural environment will not be present.Ordinarily, however, isolated antibody will be prepared by at least onepurification step.

An “isolated” nucleic acid molecule is a nucleic acid molecule that isidentified and separated from at least one contaminant nucleic acidmolecule with which it is ordinarily associated in the natural source ofthe antibody nucleic acid. An isolated nucleic acid molecule is otherthan in the form or setting in which it is found in nature. Isolatednucleic acid molecules therefore are distinguished from the nucleic acidmolecule as it exists in natural cells. However, an isolated nucleicacid molecule includes a nucleic acid molecule contained in cells thatordinarily express the antibody where, for example, the nucleic acidmolecule is in a chromosomal location different from that of naturalcells.

The term “anti-EGFL7 antibody” or “an antibody that binds to EGFL7”refers to an antibody that is capable of binding EGFL7 with sufficientaffinity such that the antibody is useful as a diagnostic and/ortherapeutic agent in targeting EGFL7. In certain embodiments, anantibody that binds to EGFL7 has a dissociation constant (Kd) of ≦1 μM,≦100 nM, ≦10 nM, ≦1 nM, or ≦0.1 nM.

“Binding affinity” generally refers to the strength of the sum total ofnoncovalent interactions between a single binding site of a molecule(e.g., an antibody) and its binding partner (e.g., an antigen). Unlessindicated otherwise, as used herein, “binding affinity” refers tointrinsic binding affinity which reflects a 1:1 interaction betweenmembers of a binding pair (e.g., antibody and antigen). The affinity ofa molecule X for its partner Y can generally be represented by thedissociation constant (Kd). Affinity can be measured by common methodsknown in the art, including those described herein. Low-affinityantibodies generally bind antigen slowly and tend to dissociate readily,whereas high-affinity antibodies generally bind antigen faster and tendto remain bound longer. A variety of methods of measuring bindingaffinity are known in the art, any of which can be used for purposes ofthe present invention. Specific illustrative embodiments are describedin the following.

In one embodiment, the “Kd” or “Kd value” according to this invention ismeasured by a radiolabeled antigen binding assay (RIA) performed withthe Fab version of an antibody of interest and its antigen as describedby the following assay that measures solution binding affinity of Fabsfor antigen by equilibrating Fab with a minimal concentration of(¹²⁵I)-labeled antigen in the presence of a titration series ofunlabeled antigen, then capturing bound antigen with an anti-Fabantibody-coated plate (Chen, et al., (1999) J. Mol. Biol 293:865-881).To establish conditions for the assay, microtiter plates (Dynex) arecoated overnight with 5 μg/ml of a capturing anti-Fab antibody (CappelLabs) in 50 mM sodium carbonate (pH 9.6), and subsequently blocked with2% (w/v) bovine serum albumin in PBS for two to five hours at roomtemperature (approximately 23° C.). In a non-adsorbant plate (Nunc#269620), 100 pM or 26 pM [¹²⁵I]-antigen are mixed with serial dilutionsof a Fab of interest (e.g., consistent with assessment of an anti-VEGFantibody, Fab-12, in Presta et al., (1997) Cancer Res. 57:4593-4599).The Fab of interest is then incubated overnight; however, the incubationmay continue for a longer period (e.g., 65 hours) to insure thatequilibrium is reached. Thereafter, the mixtures are transferred to thecapture plate for incubation at room temperature (e.g., for one hour).The solution is then removed and the plate washed eight times with 0.1%Tween™-20 in PBS. When the plates have dried, 1501/well of scintillant(MicroScint™-20; Packard) is added, and the plates are counted on aTopCount gamma counter (Packard) for ten minutes. Concentrations of eachFab that give less than or equal to 20% of maximal binding are chosenfor use in competitive binding assays. According to another embodimentthe Kd or Kd value is measured by using surface plasmon resonance assaysusing a BIAcore™-2000 or a BIAcore™-3000 (BIAcore, Inc., Piscataway,N.J.) at 25° C. with immobilized antigen CM5 chips at −10 response units(RU). Briefly, carboxymethylated dextran biosensor chips (CM5, BIAcoreInc.) are activated with N-ethyl-N′-(3-dimethylaminopropyl)-carbodiimidehydrochloride (EDC) and N-hydroxysuccinimide (NHS) according to thesupplier's instructions. Antigen is diluted with 10 mM sodium acetate,pH 4.8, into 5 μg/ml (˜0.2 μM) before injection at a flow rate of 5μl/minute to achieve approximately 10 response units (RU) of coupledprotein. Following the injection of antigen, 1M ethanolamine is injectedto block unreacted groups. For kinetics measurements, two-fold serialdilutions of Fab (0.78 nM to 500 nM) are injected in PBS with 0.05%Tween™20 (PBST) at 25° C. at a flow rate of approximately 25 μl/min.Association rates (k_(on)) and dissociation rates (k_(off)) arecalculated using a simple one-to-one Langmuir binding model (BIAcore™Evaluation Software version 3.2) by simultaneous fitting the associationand dissociation sensorgram. The equilibrium dissociation constant (Kd)is calculated as the ratio k_(off)/k_(on). See, e.g., Chen, Y., et al.,(1999) J. Mol. Biol. 293:865-881. If the on-rate exceeds 10⁶ M⁻¹ s⁻¹ bythe surface plasmon resonance assay above, then the on-rate can bedetermined by using a fluorescent quenching technique that measures theincrease or decrease in fluorescence emission intensity (excitation=295nm; emission=340 nm, 16 nm band-pass) at 25° C. of a 20 nM anti-antigenantibody (Fab form) in PBS, pH 7.2, in the presence of increasingconcentrations of antigen as measured in a spectrometer, such as astop-flow equipped spectrophotometer (Aviv Instruments) or a 8000-seriesSLM Aminco spectrophotometer (ThermoSpectronic) with a stirred cuvette.

The term “vector,” as used herein, is intended to refer to a nucleicacid molecule capable of transporting another nucleic acid to which ithas been linked. One type of vector is a “plasmid”, which refers to acircular double stranded DNA loop into which additional DNA segments maybe ligated. Another type of vector is a phage vector. Another type ofvector is a viral vector, wherein additional DNA segments may be ligatedinto the viral genome. Certain vectors are capable of autonomousreplication in a host cell into which they are introduced (e.g.,bacterial vectors having a bacterial origin of replication and episomalmammalian vectors). Other vectors (e.g., non-episomal mammalian vectors)can be integrated into the genome of a host cell upon introduction intothe host cell, and thereby are replicated along with the host genome.Moreover, certain vectors are capable of directing the expression ofgenes to which they are operatively linked. Such vectors are referred toherein as “recombinant expression vectors” (or simply, “recombinantvectors” or “expression vectors”). In general, expression vectors ofutility in recombinant DNA techniques are often in the form of plasmids.In the present specification, “plasmid” and “vector” may be usedinterchangeably.

“Polynucleotide,” or “nucleic acid,” as used interchangeably herein,refer to polymers of nucleotides of any length, and include DNA and RNA.The nucleotides can be deoxyribonucleotides, ribonucleotides, modifiednucleotides or bases, and/or their analogs, or any substrate that can beincorporated into a polymer by DNA or RNA polymerase, or by a syntheticreaction. A polynucleotide may comprise modified nucleotides, such asmethylated nucleotides and their analogs. If present, modification tothe nucleotide structure may be imparted before or after assembly of thepolymer. The sequence of nucleotides may be interrupted bynon-nucleotide components. A polynucleotide may be further modifiedafter synthesis, such as by conjugation with a label. Other types ofmodifications include, for example, “caps”, substitution of one or moreof the naturally occurring nucleotides with an analog, internucleotidemodifications such as, for example, those with uncharged linkages (e.g.,methyl phosphonates, phosphotriesters, phosphoamidates, carbamates,etc.) and with charged linkages (e.g., phosphorothioates,phosphorodithioates, etc.), those containing pendant moieties, such as,for example, proteins (e.g., nucleases, toxins, antibodies, signalpeptides, poly-L-lysine, etc.), those with intercalators (e.g.,acridine, psoralen, etc.), those containing chelators (e.g., metals,radioactive metals, boron, oxidative metals, etc.), those containingalkylators, those with modified linkages (e.g., alpha anomeric nucleicacids, etc.), as well as unmodified forms of the polynucleotide(s).Further, any of the hydroxyl groups ordinarily present in the sugars maybe replaced, for example, by phosphonate groups, phosphate groups,protected by standard protecting groups, or activated to prepareadditional linkages to additional nucleotides, or may be conjugated tosolid or semi-solid supports. The 5′ and 3′ terminal OH can bephosphorylated or substituted with amines or organic capping groupmoieties of from 1 to 20 carbon atoms. Other hydroxyls may also bederivatized to standard protecting groups. Polynucleotides can alsocontain analogous forms of ribose or deoxyribose sugars that aregenerally known in the art, including, for example, 2′-O-methyl-,2′-O-allyl, 2′-fluoro- or 2′-azido-ribose, carbocyclic sugar analogs,alpha-anomeric sugars, epimeric sugars such as arabinose, xyloses orlyxoses, pyranose sugars, furanose sugars, sedoheptuloses, acyclicanalogs and a basic nucleoside analogs such as methyl riboside. One ormore phosphodiester linkages may be replaced by alternative linkinggroups. These alternative linking groups include, but are not limitedto, embodiments wherein phosphate is replaced by P(O)S (“thioate”),P(S)S (“dithioate”), “(O)NR₂ (“amidate”), P(O)R, P(O)OR′, CO or CH₂(“formacetal”), in which each R or R′ is independently H or substitutedor unsubstituted alkyl (1-20 C) optionally containing an ether (—O—)linkage, aryl, alkenyl, cycloalkyl, cycloalkenyl or araldyl. Not alllinkages in a polynucleotide need be identical. The precedingdescription applies to all polynucleotides referred to herein, includingRNA and DNA.

“Oligonucleotide,” as used herein, generally refers to short, generallysingle stranded, generally synthetic polynucleotides that are generally,but not necessarily, less than about 200 nucleotides in length. Theterms “oligonucleotide” and “polynucleotide” are not mutually exclusive.The description above for polynucleotides is equally and fullyapplicable to oligonucleotides.

The term “EGFL7” (interchangeably termed “EGF-like-domain, multiple 7”),as used herein, refers, unless specifically or contextually indicatedotherwise, to any native or variant (whether native or synthetic) EGFL7polypeptide. The term “native sequence” specifically encompassesnaturally occurring truncated or secreted forms (e.g., an extracellulardomain sequence), naturally occurring variant forms (e.g., alternativelyspliced forms) and naturally-occurring allelic variants. The term “wildtype EGFL7” generally refers to a polypeptide comprising the amino acidsequence of a naturally occurring EGFL7 protein. The term “wild typeEGFL7 sequence” generally refers to an amino acid sequence found in anaturally occurring EGFL7.

The terms “antibody” and “immunoglobulin” are used interchangeably inthe broadest sense and include monoclonal antibodies (for e.g., fulllength or intact monoclonal antibodies), polyclonal antibodies,multivalent antibodies, multispecific antibodies (e.g., bispecificantibodies so long as they exhibit the desired biological activity) andmay also include certain antibody fragments (as described in greaterdetail herein). An antibody can be human, humanized and/or affinitymatured.

The term “variable” refers to the fact that certain portions of thevariable domains differ extensively in sequence among antibodies and areused in the binding and specificity of each particular antibody for itsparticular antigen. However, the variability is not evenly distributedthroughout the variable domains of antibodies. It is concentrated inthree segments called complementarity-determining regions orhypervariable regions (CDRs or HVRs, used interchangeably herein) bothin the light-chain and the heavy-chain variable domains. The more highlyconserved portions of variable domains are called the framework (FR).The variable domains of native heavy and light chains each comprise fourFR regions, largely adopting a β-sheet configuration, connected by threeHVRs, which form loops connecting, and in some cases forming part of,the β-sheet structure. The HVRs in each chain are held together in closeproximity by the FR regions and, with the HVRs from the other chain,contribute to the formation of the antigen-binding site of antibodies(see Kabat et al., Sequences of Proteins of Immunological Interest,Fifth Edition, National Institute of Health, Bethesda, Md. (1991)). Theconstant domains are not involved directly in binding an antibody to anantigen, but exhibit various effector functions, such as participationof the antibody in antibody-dependent cellular toxicity.

Papain digestion of antibodies produces two identical antigen-bindingfragments, called “Fab” fragments, each with a single antigen-bindingsite, and a residual “Fc” fragment, whose name reflects its ability tocrystallize readily. Pepsin treatment yields an F(ab′)₂ fragment thathas two antigen-combining sites and is still capable of cross-linkingantigen.

“Fv” is the minimum antibody fragment which contains a completeantigen-recognition and -binding site. In a two-chain Fv species, thisregion consists of a dimer of one heavy- and one light-chain variabledomain in tight, non-covalent association. In a single-chain Fv species,one heavy- and one light-chain variable domain can be covalently linkedby a flexible peptide linker such that the light and heavy chains canassociate in a “dimeric” structure analogous to that in a two-chain Fvspecies. It is in this configuration that the three HVRs of eachvariable domain interact to define an antigen-binding site on thesurface of the VH-VL dimer. Collectively, the six HVRs conferantigen-binding specificity to the antibody. However, even a singlevariable domain (or half of an Fv comprising only three HVRs specificfor an antigen) has the ability to recognize and bind antigen, althoughat a lower affinity than the entire binding site.

The Fab fragment also contains the constant domain of the light chainand the first constant domain (CH1) of the heavy chain. Fab′ fragmentsdiffer from Fab fragments by the addition of a few residues at thecarboxy terminus of the heavy chain CH1 domain including one or morecysteines from the antibody hinge region. Fab′-SH is the designationherein for Fab′ in which the cysteine residue(s) of the constant domainsbear a free thiol group. F(ab′)₂ antibody fragments originally wereproduced as pairs of Fab′ fragments which have hinge cysteines betweenthem. Other chemical couplings of antibody fragments are also known.

The “light chains” of antibodies (immunoglobulins) from any vertebratespecies can be assigned to one of two clearly distinct types, calledkappa (κ) and lambda (λ), based on the amino acid sequences of theirconstant domains.

Depending on the amino acid sequence of the constant domain of theirheavy chains, immunoglobulins can be assigned to different classes.There are five major classes of immunoglobulins: IgA, IgD, IgE, IgG, andIgM, and several of these can be further divided into subclasses(isotypes), e.g., IgG₁, IgG₂, IgG₃, IgG₄, IgA₁, and IgA₂. Theheavy-chain constant domains that correspond to the different classes ofimmunoglobulins are called α, δ, ε, γ, and μ, respectively. The subunitstructures and three-dimensional configurations of different classes ofimmunoglobulins are well known.

“Antibody fragments” comprise only a portion of an intact antibody,wherein the portion preferably retains at least one, preferably most orall, of the functions normally associated with that portion when presentin an intact antibody. Examples of antibody fragments include Fab, Fab′,F(ab′)2, and Fv fragments; diabodies; linear antibodies; single-chainantibody molecules; and multispecific antibodies formed from antibodyfragments. In one embodiment, an antibody fragment comprises an antigenbinding site of the intact antibody and thus retains the ability to bindantigen. In another embodiment, an antibody fragment, for example onethat comprises the Fc region, retains at least one of the biologicalfunctions normally associated with the Fc region when present in anintact antibody, such as FcRn binding, antibody half life modulation,ADCC function and complement binding. In one embodiment, an antibodyfragment is a monovalent antibody that has an in vivo half lifesubstantially similar to an intact antibody. For e.g., such an antibodyfragment may comprise on antigen binding arm linked to an Fc sequencecapable of conferring in vivo stability to the fragment.

The term “hypervariable region,” “HVR,” or “HV,” when used herein refersto the regions of an antibody variable domain which are hypervariable insequence and/or form structurally defined loops. Generally, antibodiescomprise six HVRs; three in the VH(H1, H2, H3), and three in the VL (L1,L2, L3). In native antibodies, H3 and L3 display the most diversity ofthe six HVRs, and H3 in particular is believed to play a unique role inconferring fine specificity to antibodies. See, e.g., Xu et al.,Immunity 13:37-45 (2000); Johnson and Wu, in Methods in MolecularBiology 248:1-25 (Lo, ed., Human Press, Totowa, N.J., 2003). Indeed,naturally occurring camelid antibodies consisting of a heavy chain onlyare functional and stable in the absence of light chain. See, e.g.,Hamers-Casterman et al., Nature 363:446-448 (1993); Sheriff et al.,Nature Struct. Biol. 3:733-736 (1996).

A number of HVR delineations are in use and are encompassed herein. TheKabat Complementarity Determining Regions (CDRs) are based on sequencevariability and are the most commonly used (Kabat et al., Sequences ofProteins of Immunological Interest, 5th Ed. Public Health Service,National Institutes of Health, Bethesda, Md. (1991)). Chothia refersinstead to the location of the structural loops (Chothia and Lesk J.Mol. Biol. 196:901-917 (1987)). The AbM HVRs represent a compromisebetween the Kabat HVRs and Chothia structural loops, and are used byOxford Molecular's AbM antibody modeling software. The “contact” HVRsare based on an analysis of the available complex crystal structures.The residues from each of these HVRs are noted below.

Loop Kabat AbM Chothia Contact L1 L24-L34 L24-L34 L26-L32 L30-L36 L2L50-L56 L50-L56 L50-L52 L46-L55 L3 L89-L97 L89-L97 L91-L96 L89-L96 H1H31-H35B H26-H35B H26-H32 H30-H35B (Kabat Numbering) H1 H31-H35 H26-H35H26-H32 H30-H35 (Chothia Numbering) H2 H50-H65 H50-H58 H53-H55 H47-H58H3 H95-H102 H95-H102 H96-H101 H93-H101

HVRs may comprise “extended HVRs” as follows: 24-36 or 24-34 (L1), 46-56or 50-56 (L2) and 89-97 or 89-96 (L3) in the VL and 26-35 (H1), 50-65 or49-65 (H2) and 93-102, 94-102, or 95-102 (H3) in the VH. The variabledomain residues are numbered according to Kabat et al., supra, for eachof these definitions.

“Framework” or “FR” residues are those variable domain residues otherthan the hypervariable region residues as herein defined.

“Humanized” forms of non-human (e.g., murine) antibodies are chimericantibodies that contain minimal sequence derived from non-humanimmunoglobulin. In one embodiment, a humanized antibody is a humanimmunoglobulin (recipient antibody) in which residues from a HVR of therecipient are replaced by residues from a HVR of a non-human species(donor antibody) such as mouse, rat, rabbit, or nonhuman primate havingthe desired specificity, affinity, and/or capacity. In some instances,FR residues of the human immunoglobulin are replaced by correspondingnon-human residues. Furthermore, humanized antibodies may compriseresidues that are not found in the recipient antibody or in the donorantibody. These modifications may be made to further refine antibodyperformance. In general, a humanized antibody will comprisesubstantially all of at least one, and typically two, variable domains,in which all or substantially all of the hypervariable loops correspondto those of a non-human immunoglobulin, and all or substantially all ofthe FRs are those of a human immunoglobulin sequence. The humanizedantibody optionally will also comprise at least a portion of animmunoglobulin constant region (Fc), typically that of a humanimmunoglobulin. For further details, see, e.g., Jones et al., Nature321:522-525 (1986); Riechmann et al., Nature 332:323-329 (1988); andPresta, Curr. Op. Struct. Biol. 2:593-596 (1992). See also, e.g.,Vaswani and Hamilton, Ann. Allergy, Asthma & Immunol. 1:105-115 (1998);Harris, Biochem. Soc. Transactions 23:1035-1038 (1995); Hurle and Gross,Curr. Op. Biotech. 5:428-433 (1994); and U.S. Pat. Nos. 6,982,321 and7,087,409.

The term “monoclonal antibody” as used herein refers to an antibodyobtained from a population of substantially homogeneous antibodies,i.e., the individual antibodies comprising the population are identicalexcept for possible mutations, e.g., naturally occurring mutations, thatmay be present in minor amounts. Thus, the modifier “monoclonal”indicates the character of the antibody as not being a mixture ofdiscrete antibodies. In certain embodiments, such a monoclonal antibodytypically includes an antibody comprising a polypeptide sequence thatbinds a target, wherein the target-binding polypeptide sequence wasobtained by a process that includes the selection of a single targetbinding polypeptide sequence from a plurality of polypeptide sequences.For example, the selection process can be the selection of a uniqueclone from a plurality of clones, such as a pool of hybridoma clones,phage clones, or recombinant DNA clones. It should be understood that aselected target binding sequence can be further altered, for example, toimprove affinity for the target, to humanize the target bindingsequence, to improve its production in cell culture, to reduce itsimmunogenicity in vivo, to create a multispecific antibody, etc., andthat an antibody comprising the altered target binding sequence is alsoa monoclonal antibody of this invention. In contrast to polyclonalantibody preparations, which typically include different antibodiesdirected against different determinants (epitopes), each monoclonalantibody of a monoclonal antibody preparation is directed against asingle determinant on an antigen. In addition to their specificity,monoclonal antibody preparations are advantageous in that they aretypically uncontaminated by other immunoglobulins.

The modifier “monoclonal” indicates the character of the antibody asbeing obtained from a substantially homogeneous population ofantibodies, and is not to be construed as requiring production of theantibody by any particular method. For example, the monoclonalantibodies to be used in accordance with the present invention may bemade by a variety of techniques, including, for example, the hybridomamethod (e.g., Kohler and Milstein, Nature, 256:495-97 (1975); Hongo etal., Hybridoma, 14 (3): 253-260 (1995), Harlow et al., Antibodies: ALaboratory Manual, (Cold Spring Harbor Laboratory Press, 2nd ed. 1988);Hammerling et al., in: Monoclonal Antibodies and T-Cell Hybridomas563-681 (Elsevier, N.Y., 1981)), recombinant DNA methods (see, e.g.,U.S. Pat. No. 4,816,567), phage-display technologies (see, e.g.,Clackson et al., Nature, 352: 624-628 (1991); Marks et al., J. Mol.Biol. 222: 581-597 (1992); Sidhu et al., J. Mol. Biol. 338(2): 299-310(2004); Lee et al., J. Mol. Biol. 340(5): 1073-1093 (2004); Fellouse,Proc. Natl. Acad. Sci. USA 101(34): 12467-12472 (2004); and Lee et al.,J. Immunol. Methods 284(1-2): 119-132 (2004), and technologies forproducing human or human-like antibodies in animals that have parts orall of the human immunoglobulin loci or genes encoding humanimmunoglobulin sequences (see, e.g., WO 1998/24893; WO 1996/34096; WO1996/33735; WO 1991/10741; Jakobovits et al., Proc. Natl. Acad. Sci. USA90: 2551 (1993); Jakobovits et al., Nature 362: 255-258 (1993);Bruggemann et al., Year in Immunol. 7:33 (1993); U.S. Pat. Nos.5,545,807; 5,545,806; 5,569,825; 5,625,126; 5,633,425; and 5,661,016;Marks et al., Bio/Technology 10: 779-783 (1992); Lonberg et al., Nature368: 856-859 (1994); Morrison, Nature 368: 812-813 (1994); Fishwild etal., Nature Biotechnol. 14: 845-851 (1996); Neuberger, NatureBiotechnol. 14: 826 (1996); and Lonberg and Huszar, Intern. Rev.Immunol. 13: 65-93 (1995).

The monoclonal antibodies herein specifically include “chimeric”antibodies in which a portion of the heavy and/or light chain isidentical with or homologous to corresponding sequences in antibodiesderived from a particular species or belonging to a particular antibodyclass or subclass, while the remainder of the chain(s) is identical withor homologous to corresponding sequences in antibodies derived fromanother species or belonging to another antibody class or subclass, aswell as fragments of such antibodies, so long as they exhibit thedesired biological activity (see, e.g., U.S. Pat. No. 4,816,567; andMorrison et al., Proc. Natl. Acad. Sci. USA 81:6851-6855 (1984)).Chimeric antibodies include PRIMATIZED® antibodies wherein theantigen-binding region of the antibody is derived from an antibodyproduced by, e.g., immunizing macaque monkeys with the antigen ofinterest.

“Single-chain Fv” or “scFv” antibody fragments comprise the VH and VLdomains of antibody, wherein these domains are present in a singlepolypeptide chain. Generally, the scFv polypeptide further comprises apolypeptide linker between the VH and VL domains which enables the scFvto form the desired structure for antigen binding. For a review of scFvsee Pluckthun, in The Pharmacology of Monoclonal Antibodies, vol. 113,Rosenburg and Moore eds., Springer-Verlag, New York, pp. 269-315 (1994).

An “antigen” is a predetermined antigen to which an antibody canselectively bind. The target antigen may be polypeptide, carbohydrate,nucleic acid, lipid, hapten or other naturally occurring or syntheticcompound.

The term “diabodies” refers to small antibody fragments with twoantigen-binding sites, which fragments comprise a heavy-chain variabledomain (VH) connected to a light-chain variable domain (VL) in the samepolypeptide chain (VH-VL). By using a linker that is too short to allowpairing between the two domains on the same chain, the domains areforced to pair with the complementary domains of another chain andcreate two antigen-binding sites. Diabodies are described more fully in,for example, EP 404,097; WO 93/11161; and Hollinger et al., Proc. Natl.Acad. Sci. USA, 90:6444-6448 (1993). Triabodies and tetrabodies are alsodescribed in Hudson et al., Nat. Med. 9:129-134 (2003).

A “human antibody” is one which possesses an amino acid sequence whichcorresponds to that of an antibody produced by a human and/or has beenmade using any of the techniques for making human antibodies asdisclosed herein. This definition of a human antibody specificallyexcludes a humanized antibody comprising non-human antigen-bindingresidues. Human antibodies can be produced using various techniquesknown in the art, including phage-display libraries. Hoogenboom andWinter, J. Mol. Biol., 227:381 (1991); Marks et al., J. Mol. Biol.,222:581 (1991). Also available for the preparation of human monoclonalantibodies are methods described in Cole et al., Monoclonal Antibodiesand Cancer Therapy, Alan R. Liss, p. 77 (1985); Boerner et al., J.Immunol., 147(1):86-95 (1991). See also van Dijk and van de Winkel,Curr. Opin. Pharmacol., 5: 368-74 (2001). Human antibodies can beprepared by administering the antigen to a transgenic animal that hasbeen modified to produce such antibodies in response to antigenicchallenge, but whose endogenous loci have been disabled, e.g., immunizedxenomice (see, e.g., U.S. Pat. Nos. 6,075,181 and 6,150,584 regardingXENOMOUSE™ technology). See also, for example, Li et al., Proc. Natl.Acad. Sci. USA, 103:3557-3562 (2006) regarding human antibodiesgenerated via a human B-cell hybridoma technology.

The term “variable domain residue numbering as in Kabat” or “amino acidposition numbering as in Kabat,” and variations thereof, refers to thenumbering system used for heavy chain variable domains or light chainvariable domains of the compilation of antibodies in Kabat et al.,supra. Using this numbering system, the actual linear amino acidsequence may contain fewer or additional amino acids corresponding to ashortening of, or insertion into, a FR or HVR of the variable domain.For example, a heavy chain variable domain may include a single aminoacid insert (residue 52a according to Kabat) after residue 52 of H2 andinserted residues (e.g. residues 82a, 82b, and 82c, etc. according toKabat) after heavy chain FR residue 82. The Kabat numbering of residuesmay be determined for a given antibody by alignment at regions ofhomology of the sequence of the antibody with a “standard” Kabatnumbered sequence.

The Kabat numbering system is generally used when referring to a residuein the variable domain (approximately residues 1-107 of the light chainand residues 1-113 of the heavy chain) (e.g, Kabat et al., Sequences ofImmunological Interest. 5th Ed. Public Health Service, NationalInstitutes of Health, Bethesda, Md. (1991)). The “EU numbering system”or “EU index” is generally used when referring to a residue in animmunoglobulin heavy chain constant region (e.g., the EU index reportedin Kabat et al., supra). The “EU index as in Kabat” refers to theresidue numbering of the human IgG₁ EU antibody. Unless stated otherwiseherein, references to residue numbers in the variable domain ofantibodies means residue numbering by the Kabat numbering system. Unlessstated otherwise herein, references to residue numbers in the constantdomain of antibodies means residue numbering by the EU numbering system(e.g., see U.S. Provisional Application No. 60/640,323, Figures for EUnumbering).

A “blocking” antibody or an “antagonist” antibody is one which inhibitsor reduces biological activity of the antigen it binds. Certain blockingantibodies or antagonist antibodies substantially or completely inhibitthe biological activity of the antigen.

The term “substantially similar” or “substantially the same,” as usedherein, denotes a sufficiently high degree of similarity between twonumeric values (for example, one associated with an antibody of theinvention and the other associated with a reference/comparatorantibody), such that one of skill in the art would consider thedifference between the two values to be of little or no biologicaland/or statistical significance within the context of the biologicalcharacteristic measured by said values (e.g., Kd values). The differencebetween said two values is, for example, less than about 50%, less thanabout 40%, less than about 30%, less than about 20%, and/or less thanabout 10% as a function of the reference/comparator value.

The phrase “substantially reduced,” or “substantially different,” asused herein, denotes a sufficiently high degree of difference betweentwo numeric values (generally one associated with a molecule and theother associated with a reference/comparator molecule) such that one ofskill in the art would consider the difference between the two values tobe of statistical significance within the context of the biologicalcharacteristic measured by said values (e.g., Kd values). The differencebetween said two values is, for example, greater than about 10%, greaterthan about 20%, greater than about 30%, greater than about 40%, and/orgreater than about 50% as a function of the value for thereference/comparator molecule.

Antibody “effector functions” refer to those biological activitiesattributable to the Fc region (a native sequence Fc region or amino acidsequence variant Fc region) of an antibody, and vary with the antibodyisotype. Examples of antibody effector functions include: Clq bindingand complement dependent cytotoxicity (CDC); Fc receptor binding;antibody-dependent cell-mediated cytotoxicity (ADCC); phagocytosis; downregulation of cell surface receptors (e.g. B cell receptor); and B cellactivation.

The term “Fc region” herein is used to define a C-terminal region of animmunoglobulin heavy chain, including native sequence Fc regions andvariant Fc regions. Although the boundaries of the Fc region of animmunoglobulin heavy chain might vary, the human IgG heavy chain Fcregion is usually defined to stretch from an amino acid residue atposition Cys226, or from Pro230, to the carboxyl-terminus thereof. TheC-terminal lysine (residue 447 according to the EU numbering system) ofthe Fc region may be removed, for example, during production orpurification of the antibody, or by recombinantly engineering thenucleic acid encoding a heavy chain of the antibody. Accordingly, acomposition of intact antibodies may comprise antibody populations withall K447 residues removed, antibody populations with no K447 residuesremoved, and antibody populations having a mixture of antibodies withand without the K447 residue.

A “functional Fc region” possesses an “effector function” of a nativesequence Fc region. Exemplary “effector functions” include Clq binding;CDC; Fc receptor binding; ADCC; phagocytosis; down regulation of cellsurface receptors (e.g. B cell receptor; BCR), etc. Such effectorfunctions generally require the Fc region to be combined with a bindingdomain (e.g., an antibody variable domain) and can be assessed usingvarious assays as disclosed, for example, in definitions herein.

A “native sequence Fc region” comprises an amino acid sequence identicalto the amino acid sequence of an Fc region found in nature. Nativesequence human Fc regions include a native sequence human IgG1 Fc region(non-A and A allotypes); native sequence human IgG2 Fc region; nativesequence human IgG3 Fc region; and native sequence human IgG4 Fc regionas well as naturally occurring variants thereof.

A “variant Fc region” comprises an amino acid sequence which differsfrom that of a native sequence Fc region by virtue of at least one aminoacid modification, preferably one or more amino acid substitution(s).Preferably, the variant Fc region has at least one amino acidsubstitution compared to a native sequence Fc region or to the Fc regionof a parent polypeptide, e.g. from about one to about ten amino acidsubstitutions, and preferably from about one to about five amino acidsubstitutions in a native sequence Fc region or in the Fc region of theparent polypeptide. The variant Fc region herein will preferably possessat least about 80% homology with a native sequence Fc region and/or withan Fc region of a parent polypeptide, and most preferably at least about90% homology therewith, more preferably at least about 95% homologytherewith.

“Fc receptor” or “FcR” describes a receptor that binds to the Fc regionof an antibody. In some embodiments, an FcR is a native human FcR. Insome embodiments, an FcR is one which binds an IgG antibody (a gammareceptor) and includes receptors of the FcγRI, FcγRII, and FcγRIIIsubclasses, including allelic variants and alternatively spliced formsof those receptors. FcγRII receptors include FcγRIIA (an “activatingreceptor”) and FcγRIIB (an “inhibiting receptor”), which have similaramino acid sequences that differ primarily in the cytoplasmic domainsthereof. Activating receptor FcγRIIA contains an immunoreceptortyrosine-based activation motif (ITAM) in its cytoplasmic domain.Inhibiting receptor FcγRIIB contains an immunoreceptor tyrosine-basedinhibition motif (ITIM) in its cytoplasmic domain. (see, e.g., Daëron,Annu. Rev. Immunol. 15:203-234 (1997)). FcRs are reviewed, for example,in Ravetch and Kinet, Annu. Rev. Immunol 9:457-92 (1991); Capel et al.,Immunomethods 4:25-34 (1994); and de Haas et al., J. Lab. Clin. Med.126:330-41 (1995). Other FcRs, including those to be identified in thefuture, are encompassed by the term “FcR” herein.

The term “Fc receptor” or “FcR” also includes the neonatal receptor,FcRn, which is responsible for the transfer of maternal IgGs to thefetus (Guyer et al., J. Immunol. 117:587 (1976) and Kim et al., J.Immunol. 24:249 (1994)) and regulation of homeostasis ofimmunoglobulins. Methods of measuring binding to FcRn are known (see,e.g., Ghetie and Ward., Immunol. Today 18(12):592-598 (1997); Ghetie etal., Nature Biotechnology, 15(7):637-640 (1997); Hinton et al., J. Biol.Chem. 279(8):6213-6216 (2004); WO 2004/92219 (Hinton et al.).

Binding to human FcRn in vivo and serum half life of human FcRn highaffinity binding polypeptides can be assayed, e.g., in transgenic miceor transfected human cell lines expressing human FcRn, or in primates towhich the polypeptides with a variant Fc region are administered. WO2000/42072 (Presta) describes antibody variants with improved ordiminished binding to FcRs. See also, e.g., Shields et al. J. Biol.Chem. 9(2):6591-6604 (2001).

“Human effector cells” are leukocytes which express one or more FcRs andperform effector functions. In certain embodiments, the cells express atleast FcγRIII and perform ADCC effector function(s). Examples of humanleukocytes which mediate ADCC include peripheral blood mononuclear cells(PBMC), natural killer (NK) cells, monocytes, cytotoxic T cells, andneutrophils. The effector cells may be isolated from a native source,e.g., from blood.

“Antibody-dependent cell-mediated cytotoxicity” or “ADCC” refers to aform of cytotoxicity in which secreted Ig bound onto Fc receptors (FcRs)present on certain cytotoxic cells (e.g. NK cells, neutrophils, andmacrophages) enable these cytotoxic effector cells to bind specificallyto an antigen-bearing target cell and subsequently kill the target cellwith cytotoxins. The primary cells for mediating ADCC, NK cells, expressFcγRIII only, whereas monocytes express FcγRI, FcγRII, and FcγRIII. FcRexpression on hematopoietic cells is summarized in Table 3 on page 464of Ravetch and Kinet, Annu. Rev. Immunol 9:457-92 (1991). To assess ADCCactivity of a molecule of interest, an in vitro ADCC assay, such as thatdescribed in U.S. Pat. No. 5,500,362 or 5,821,337 or U.S. Pat. No.6,737,056 (Presta), may be performed. Useful effector cells for suchassays include PBMC and NK cells. Alternatively, or additionally, ADCCactivity of the molecule of interest may be assessed in vivo, e.g., inan animal model such as that disclosed in Clynes et al. PNAS (USA)95:652-656 (1998).

“Complement dependent cytotoxicity” or “CDC” refers to the lysis of atarget cell in the presence of complement. Activation of the classicalcomplement pathway is initiated by the binding of the first component ofthe complement system (Clq) to antibodies (of the appropriate subclass),which are bound to their cognate antigen. To assess complementactivation, a CDC assay, e.g., as described in Gazzano-Santoro et al.,J. Immunol. Methods 202:163 (1996), may be performed. Polypeptidevariants with altered Fc region amino acid sequences (polypeptides witha variant Fc region) and increased or decreased Clq binding capabilityare described, e.g., in U.S. Pat. No. 6,194,551 B1 and WO 1999/51642.See also, e.g., Idusogie et al. J. Immunol. 164: 4178-4184 (2000).

The term “Fc region-comprising antibody” refers to an antibody thatcomprises an Fc region. The C-terminal lysine (residue 447 according tothe EU numbering system) of the Fc region may be removed, for example,during purification of the antibody or by recombinant engineering of thenucleic acid encoding the antibody. Accordingly, a compositioncomprising an antibody having an Fc region according to this inventioncan comprise an antibody with K447, with all K447 removed, or a mixtureof antibodies with and without the K447 residue.

An “acceptor human framework” for the purposes herein is a frameworkcomprising the amino acid sequence of a VL or VH framework derived froma human immunoglobulin framework, or from a human consensus framework.An acceptor human framework “derived from” a human immunoglobulinframework or human consensus framework may comprise the same amino acidsequence thereof, or may contain pre-existing amino acid sequencechanges. Where pre-existing amino acid changes are present, preferablyno more than 5 and preferably 4 or less, or 3 or less, pre-existingamino acid changes are present. Where pre-existing amino acid changesare present in a VH, preferably those changes are only at three, two orone of positions 71H, 73H and 78H; for instance, the amino acid residuesat those positions may be 71A, 73T and/or 78A. In one embodiment, the VLacceptor human framework is identical in sequence to the VL humanimmunoglobulin framework sequence or human consensus framework sequence.

A “human consensus framework” is a framework which represents the mostcommonly occurring amino acid residue in a selection of humanimmunoglobulin VL or VH framework sequences. Generally, the selection ofhuman immunoglobulin VL or VH sequences is from a subgroup of variabledomain sequences. Generally, the subgroup of sequences is a subgroup asin Kabat et al. In one embodiment, for the VL, the subgroup is subgroupkappa I as in Kabat et al. In one embodiment, for the VH, the subgroupis subgroup III as in Kabat et al.

A “VH subgroup III consensus framework” comprises the consensus sequenceobtained from the amino acid sequences in variable heavy subgroup III ofKabat et al. In one embodiment, the VH subgroup III consensus frameworkamino acid sequence comprises at least a portion or all of each of thefollowing sequences:

(SEQ ID NO: 197) EVQLVESGGGLVQPGGSLRLSCAAS- (SEQ ID NO: 198)H1-WVRQAPGKGLEWV- (SEQ ID NO: 199 H2-RFTISRDNSKNTLYLQMNSLRAEDTAVYYC-(SEQ ID NO: 200) H3-WGQGTLVTVSS.

A “VL subgroup I consensus framework” comprises the consensus sequenceobtained from the amino acid sequences in variable light kappa subgroupI of Kabat et al.

In one embodiment, the VH subgroup I consensus framework amino acidsequence comprises at least a portion or all of each of the followingsequences:

(SEQ ID NO: 201) DIQMTQSPSSLSASVGDRVTITC- (SEQ ID NO: 202)L1-WYQQKPGKAPKLLIY- (SEQ ID NO: 203)L2-GVPSRFSGSGSGTDFTLTISSLQPEDFATYYC- (SEQ ID NO: 221) L3-FGQGTKVEIK.

A “biological sample” (interchangeably termed “sample” or “tissue orcell sample”) encompasses a variety of sample types obtained from anindividual and can be used in a diagnostic or monitoring assay. Thedefinition encompasses blood and other liquid samples of biologicalorigin, solid tissue samples such as a biopsy specimen or tissuecultures or cells derived therefrom, and the progeny thereof. Thedefinition also includes samples that have been manipulated in any wayafter their procurement, such as by treatment with reagents,solubilization, or enrichment for certain components, such as proteinsor polynucleotides, or embedding in a semi-solid or solid matrix forsectioning purposes. The term “biological sample” encompasses a clinicalsample, and also includes cells in culture, cell supernatants, celllysates, serum, plasma, biological fluid, and tissue samples. The sourceof the biological sample may be solid tissue as from a fresh, frozenand/or preserved organ or tissue sample or biopsy or aspirate; blood orany blood constituents; bodily fluids such as cerebral spinal fluid,amniotic fluid, peritoneal fluid, or interstitial fluid; cells from anytime in gestation or development of the subject. In some embodiments,the biological sample is obtained from a primary or metastatic tumor.The biological sample may contain compounds which are not naturallyintermixed with the tissue in nature such as preservatives,anticoagulants, buffers, fixatives, nutrients, antibiotics, or the like.

For the purposes herein a “section” of a tissue sample is meant a singlepart or piece of a tissue sample, e.g. a thin slice of tissue or cellscut from a tissue sample. It is understood that multiple sections oftissue samples may be taken and subjected to analysis according to thepresent invention. In some embodiments, the same section of tissuesample is analyzed at both morphological and molecular levels, or isanalyzed with respect to both protein and nucleic acid.

The word “label” when used herein refers to a compound or compositionwhich is conjugated or fused directly or indirectly to a reagent such asa nucleic acid probe or an antibody and facilitates detection of thereagent to which it is conjugated or fused. The label may itself bedetectable (e.g., radioisotope labels or fluorescent labels) or, in thecase of an enzymatic label, may catalyze chemical alteration of asubstrate compound or composition which is detectable.

A “medicament” is an active drug to treat the disorder in question orits symptoms, or side effects.

A “disorder” or “disease” is any condition that would benefit fromtreatment with a substance/molecule or method of the invention. Thisincludes chronic and acute disorders or diseases including thosepathological conditions which predispose the mammal to the disorder inquestion. Non-limiting examples of disorders to be treated hereininclude malignant and benign tumors; carcinoma, blastoma, and sarcoma.

The terms “cell proliferative disorder” and “proliferative disorder”refer to disorders that are associated with some degree of abnormal cellproliferation. In one embodiment, the cell proliferative disorder iscancer.

“Tumor”, as used herein, refers to all neoplastic cell growth andproliferation, whether malignant or benign, and all pre-cancerous andcancerous cells and tissues. The terms “cancer”, “cancerous”, “cellproliferative disorder”, “proliferative disorder” and “tumor” are notmutually exclusive as referred to herein.

The terms “cancer” and “cancerous” refer to or describe thephysiological condition in mammals that is typically characterized byunregulated cell growth/proliferation. Examples of cancer include butare not limited to, carcinoma, lymphoma, blastoma, sarcoma, andleukemia. More particular examples of such cancers include squamous cellcancer, small-cell lung cancer, pituitary cancer, esophageal cancer,astrocytoma, soft tissue sarcoma, non-small cell lung cancer,adenocarcinoma of the lung, squamous carcinoma of the lung, cancer ofthe peritoneum, hepatocellular cancer, gastrointestinal cancer,pancreatic cancer, glioblastoma, cervical cancer, ovarian cancer, livercancer, bladder cancer, hepatoma, breast cancer, colon cancer,colorectal cancer, endometrial or uterine carcinoma, salivary glandcarcinoma, kidney cancer, liver cancer, prostate cancer, vulval cancer,thyroid cancer, hepatic carcinoma, brain cancer, endometrial cancer,testis cancer, cholangiocarcinoma, gallbladder carcinoma, gastriccancer, melanoma, and various types of head and neck cancer.Dysregulation of angiogenesis can lead to many disorders that can betreated by compositions and methods of the invention. These disordersinclude both non-neoplastic and neoplastic conditions. Neoplasticsinclude but are not limited those described above. Non-neoplasticdisorders include but are not limited to undesired or aberranthypertrophy, arthritis, rheumatoid arthritis (RA), psoriasis, psoriaticplaques, sarcoidosis, atherosclerosis, atherosclerotic plaques, diabeticand other proliferative retinopathies including retinopathy ofprematurity, retrolental fibroplasia, neovascular glaucoma, age-relatedmacular degeneration, diabetic macular edema, cornealneovascularization, corneal graft neovascularization, corneal graftrejection, retinal/choroidal neovascularization, neovascularization ofthe angle (rubeosis), ocular neovascular disease, vascular restenosis,arteriovenous malformations (AVM), meningioma, hemangioma, angiofibroma,thyroid hyperplasias (including Grave's disease), corneal and othertissue transplantation, chronic inflammation, lung inflammation, acutelung injury/ARDS, sepsis, primary pulmonary hypertension, malignantpulmonary effusions, cerebral edema (e.g., associated with acutestroke/closed head injury/trauma), synovial inflammation, pannusformation in RA, myositis ossificans, hypertropic bone formation,osteoarthritis (OA), refractory ascites, polycystic ovarian disease,endometriosis, 3rd spacing of fluid diseases (pancreatitis, compartmentsyndrome, burns, bowel disease), uterine fibroids, premature labor,chronic inflammation such as IBD (Crohn's disease and ulcerativecolitis), renal allograft rejection, inflammatory bowel disease,nephrotic syndrome, undesired or aberrant tissue mass growth(non-cancer), hemophilic joints, hypertrophic scars, inhibition of hairgrowth, Osler-Weber syndrome, pyogenic granuloma retrolentalfibroplasias, scleroderma, trachoma, vascular adhesions, synovitis,dermatitis, preeclampsia, ascites, pericardial effusion (such as thatassociated with pericarditis), and pleural effusion.

The term “wasting” disorders (e.g., wasting syndrome, cachexia,sarcopenia) refers to a disorder caused by undesirable and/or unhealthyloss of weight or loss of body cell mass. In the elderly as well as inAIDS and cancer patients, wasting disease can result in undesired lossof body weight, including both the fat and the fat-free compartments.Wasting diseases can be the result of inadequate intake of food and/ormetabolic changes related to illness and/or the aging process. Cancerpatients and AIDS patients, as well as patients following extensivesurgery or having chronic infections, immunologic diseases,hyperthyroidism, Crohn's disease, psychogenic disease, chronic heartfailure or other severe trauma, frequently suffer from wasting diseasewhich is sometimes also referred to as cachexia, a metabolic and,sometimes, an eating disorder. Cachexia is additionally characterized byhypermetabolism and hypercatabolism. Although cachexia and wastingdisease are frequently used interchangeably to refer to wastingconditions, there is at least one body of research which differentiatescachexia from wasting syndrome as a loss of fat-free mass, andparticularly, body cell mass (Mayer, 1999, J. Nutr. 129(1SSuppl.):256S-259S). Sarcopenia, yet another such disorder which canaffect the aging individual, is typically characterized by loss ofmuscle mass. End stage wasting disease as described above can develop inindividuals suffering from either cachexia or sarcopenia.

As used herein, “treatment” refers to clinical intervention in anattempt to alter the natural course of the individual or cell beingtreated, and can be performed either for prophylaxis or during thecourse of clinical pathology. Desirable effects of treatment includepreventing occurrence or recurrence of disease, alleviation of symptoms,diminishment of any direct or indirect pathological consequences of thedisease, decreasing the rate of disease progression, amelioration orpalliation of the disease state, and remission or improved prognosis. Insome embodiments, antibodies of the invention are used to delaydevelopment of a disease or disorder.

An “anti-angiogenesis agent” or “angiogenesis inhibitor” refers to asmall molecular weight substance, a polynucleotide, a polypeptide, anisolated protein, a recombinant protein, an antibody, or conjugates orfusion proteins thereof, that inhibits angiogenesis, vasculogenesis, orundesirable vascular permeability, either directly or indirectly. Forexample, an anti-angiogenesis agent is an antibody or other antagonistto an angiogenic agent as defined above, e.g., antibodies to VEGF,antibodies to VEGF receptors, small molecules that block VEGF receptorsignaling (e.g., PTK787/ZK2284, SU6668, SUTENT®/SU11248 (sunitinibmalate), AMG706). Anti-angiogenesis agents also include nativeangiogenesis inhibitors, e.g., angiostatin, endostatin, etc. See, e.g.,Klagsbrun and D'Amore, Annu. Rev. Physiol., 53:217-39 (1991); Streit andDetmar, Oncogene, 22:3172-3179 (2003) (e.g., Table 3 listinganti-angiogenic therapy in malignant melanoma); Ferrara & Alitalo,Nature Medicine 5(12):1359-1364 (1999); Tonini et al., Oncogene,22:6549-6556 (2003) (e.g., Table 2 listing antiangiogenic factors); and,Sato Int. J. Clin. Oncol., 8:200-206 (2003) (e.g., Table 1 listsAnti-angiogenic agents used in clinical trials).

An “individual,” “subject,” or “patient” is a vertebrate. In certainembodiments, the vertebrate is a mammal. Mammals include, but are notlimited to, farm animals (such as cows), sport animals, pets (such ascats, dogs, and horses), primates, mice and rats. In certainembodiments, a mammal is a human.

An “effective amount” refers to an amount effective, at dosages and forperiods of time necessary, to achieve the desired therapeutic orprophylactic result.

A “therapeutically effective amount” of a substance/molecule of theinvention, agonist or antagonist may vary according to factors such asthe disease state, age, sex, and weight of the individual, and theability of the substance/molecule, agonist or antagonist to elicit adesired response in the individual. A therapeutically effective amountis also one in which any toxic or detrimental effects of thesubstance/molecule, agonist or antagonist are outweighed by thetherapeutically beneficial effects. A “prophylactically effectiveamount” refers to an amount effective, at dosages and for periods oftime necessary, to achieve the desired prophylactic result. Typicallybut not necessarily, since a prophylactic dose is used in subjects priorto or at an earlier stage of disease, the prophylactically effectiveamount will be less than the therapeutically effective amount.

The term “cytotoxic agent” as used herein refers to a substance thatinhibits or prevents the function of cells and/or causes destruction ofcells. The term is intended to include radioactive isotopes (e.g.,At²¹¹, I¹³¹, I¹²⁵, Y⁹⁰, Re¹⁸⁶, Re¹⁸⁸, Sm¹⁵³, Bi²¹², P³² and radioactiveisotopes of Lu), chemotherapeutic agents e.g. methotrexate, adriamicin,vinca alkaloids (vincristine, vinblastine, etoposide), doxorubicin,melphalan, mitomycin C, chlorambucil, daunorubicin or otherintercalating agents, enzymes and fragments thereof such as nucleolyticenzymes, antibiotics, and toxins such as small molecule toxins orenzymatically active toxins of bacterial, fungal, plant or animalorigin, including fragments and/or variants thereof, and the variousantitumor or anticancer agents disclosed below. Other cytotoxic agentsare described below. A tumoricidal agent causes destruction of tumorcells.

A “toxin” is any substance capable of having a detrimental effect on thegrowth or proliferation of a cell.

A “chemotherapeutic agent” is a chemical compound useful in thetreatment of cancer. Examples of chemotherapeutic agents includealkylating agents such as thiotepa and cyclosphosphamide (CYTOXAN®);alkyl sulfonates such as busulfan, improsulfan and piposulfan;aziridines such as benzodopa, carboquone, meturedopa, and uredopa;ethylenimines and methylamelamines including altretamine,triethylenemelamine, triethylenephosphoramide,triethylenethiophosphoramide and trimethylomelamine; acetogenins(especially bullatacin and bullatacinone); delta-9-tetrahydrocannabinol(dronabinol, MARINOL®); beta-lapachone; lapachol; colchicines; betulinicacid; a camptothecin (including the synthetic analogue topotecan(HYCAMTIN®), CPT-11 (irinotecan, CAMPTOSAR®), acetylcamptothecin,scopolectin, and 9-aminocamptothecin); bryostatin; callystatin; CC-1065(including its adozelesin, carzelesin and bizelesin syntheticanalogues); podophyllotoxin; podophyllinic acid; teniposide;cryptophycins (particularly cryptophycin 1 and cryptophycin 8);dolastatin; duocarmycin (including the synthetic analogues, KW-2189 andCB1-TM1); eleutherobin; pancratistatin; a sarcodictyin; spongistatin;nitrogen mustards such as chlorambucil, chlornaphazine,chlorophosphamide, estramustine, ifosfamide, mechlorethamine,mechlorethamine oxide hydrochloride, melphalan, novembichin,phenesterine, prednimustine, trofosfamide, uracil mustard; nitrosoureassuch as carmustine, chlorozotocin, fotemustine, lomustine, nimustine,and ranimnustine; antibiotics such as the enediyne antibiotics (e.g.,calicheamicin, especially calicheamicin gamma1I and calicheamicinomegaI1 (see, e.g., Nicolaou et al., Angew. Chem. Intl. Ed. Engl., 33:183-186 (1994)); CDP323, an oral alpha-4 integrin inhibitor; dynemicin,including dynemicin A; an esperamicin; as well as neocarzinostatinchromophore and related chromoprotein enediyne antibiotic chromophores),aclacinomysins, actinomycin, authramycin, azaserine, bleomycins,cactinomycin, carabicin, caminomycin, carzinophilin, chromomycins,dactinomycin, daunorubicin, detorubicin, 6-diazo-5-oxo-L-norleucine,doxorubicin (including ADRIAMYCIN®, morpholino-doxorubicin,cyanomorpholino-doxorubicin, 2-pyrrolino-doxorubicin, doxorubicin HClliposome injection (DOXIL®), liposomal doxorubicin TLC D-99 (MYOCET®),peglylated liposomal doxorubicin (CAELYX®), and deoxydoxorubicin),epirubicin, esorubicin, idarubicin, marcellomycin, mitomycins such asmitomycin C, mycophenolic acid, nogalamycin, olivomycins, peplomycin,porfiromycin, puromycin, quelamycin, rodorubicin, streptonigrin,streptozocin, tubercidin, ubenimex, zinostatin, zorubicin;anti-metabolites such as methotrexate, gemcitabine (GEMZAR®), tegafur(UFTORAL®), capecitabine (XELODA®), an epothilone, and 5-fluorouracil(5-FU); folic acid analogues such as denopterin, methotrexate,pteropterin, trimetrexate; purine analogs such as fludarabine,6-mercaptopurine, thiamiprine, thioguanine; pyrimidine analogs such asancitabine, azacitidine, 6-azauridine, carmofur, cytarabine,dideoxyuridine, doxifluridine, enocitabine, floxuridine; androgens suchas calusterone, dromostanolone propionate, epitiostanol, mepitiostane,testolactone; anti-adrenals such as aminoglutethimide, mitotane,trilostane; folic acid replenisher such as frolinic acid; aceglatone;aldophosphamide glycoside; aminolevulinic acid; eniluracil; amsacrine;bestrabucil; bisantrene; edatraxate; defofamine; demecolcine;diaziquone; elfornithine; elliptinium acetate; an epothilone; etoglucid;gallium nitrate; hydroxyurea; lentinan; lonidainine; maytansinoids suchas maytansine and ansamitocins; mitoguazone; mitoxantrone; mopidanmol;nitraerine; pentostatin; phenamet; pirarubicin; losoxantrone;2-ethylhydrazide; procarbazine; PSK® polysaccharide complex (JHS NaturalProducts, Eugene, Oreg.); razoxane; rhizoxin; sizofuran; spirogermanium;tenuazonic acid; triaziquone; 2,2′,2′-trichlorotriethylamine;trichothecenes (especially T-2 toxin, verracurin A, roridin A andanguidine); urethan; vindesine (ELDISINE®, FILDESIN®); dacarbazine;mannomustine; mitobronitol; mitolactol; pipobroman; gacytosine;arabinoside (“Ara-C”); thiotepa; taxoid, e.g., paclitaxel (TAXOL®),albumin-engineered nanoparticle formulation of paclitaxel (ABRAXANE™),and docetaxel (TAXOTERE®); chloranbucil; 6-thioguanine; mercaptopurine;methotrexate; platinum agents such as cisplatin, oxaliplatin (e.g.,ELOXATIN®), and carboplatin; vincas, which prevent tubulinpolymerization from forming microtubules, including vinblastine(VELBAN®), vincristine (ONCOVIN®), vindesine (ELDISINE®, FILDESIN®), andvinorelbine (NAVELBINE®); etoposide (VP-16); ifosfamide; mitoxantrone;leucovorin; novantrone; edatrexate; daunomycin; aminopterin;ibandronate; topoisomerase inhibitor RFS 2000; difluoromethylomithine(DMFO); retinoids such as retinoic acid, including bexarotene(TARGRETIN®); bisphosphonates such as clodronate (for example, BONEFOS®or OSTAC®), etidronate (DIDROCAL®), NE-58095, zoledronicacid/zoledronate (ZOMETA®), alendronate (FOSAMAX®), pamidronate(AREDIA®), tiludronate (SKELID®), or risedronate (ACTONEL®);troxacitabine (a 1,3-dioxolane nucleoside cytosine analog); antisenseoligonucleotides, particularly those that inhibit expression of genes insignaling pathways implicated in aberrant cell proliferation, such as,for example, PKC-alpha, Raf, H-Ras, and epidermal growth factor receptor(EGF-R); vaccines such as THERATOPE® vaccine and gene therapy vaccines,for example, ALLOVECTIN® vaccine, LEUVECTIN® vaccine, and VAXID®vaccine; topoisomerase 1 inhibitor (e.g., LURTOTECAN®); rmRH (e.g.,ABARELIX®); BAY439006 (sorafenib; Bayer); SU-11248 (sunitinib, SUTENT®,Pfizer); perifosine, COX-2 inhibitor (e.g. celecoxib or etoricoxib),proteosome inhibitor (e.g. PS341); bortezomib (VELCADE®); CCI-779;tipifarnib (R11577); orafenib, ABT510; Bcl-2 inhibitor such asoblimersen sodium (GENASENSE®); pixantrone; EGFR inhibitors (seedefinition below); tyrosine kinase inhibitors (see definition below);serine-threonine kinase inhibitors such as rapamycin (sirolimus,RAPAMUNE®); farnesyltransferase inhibitors such as lonafamib (SCH 6636,SARASAR™); and pharmaceutically acceptable salts, acids or derivativesof any of the above; as well as combinations of two or more of the abovesuch as CHOP, an abbreviation for a combined therapy ofcyclophosphamide, doxorubicin, vincristine, and prednisolone; andFOLFOX, an abbreviation for a treatment regimen with oxaliplatin(ELOXATIN™) combined with 5-FU and leucovorin.

Chemotherapeutic agents as defined herein include “anti-hormonal agents”or “endocrine therapeutics” which act to regulate, reduce, block, orinhibit the effects of hormones that can promote the growth of cancer.They may be hormones themselves, including, but not limited to:anti-estrogens with mixed agonist/antagonist profile, including,tamoxifen (NOLVADEX®), 4-hydroxytamoxifen, toremifene (FARESTON®),idoxifene, droloxifene, raloxifene (EVISTA®), trioxifene, keoxifene, andselective estrogen receptor modulators (SERMs) such as SERM3; pureanti-estrogens without agonist properties, such as fulvestrant(FASLODEX®), and EM800 (such agents may block estrogen receptor (ER)dimerization, inhibit DNA binding, increase ER turnover, and/or suppressER levels); aromatase inhibitors, including steroidal aromataseinhibitors such as formestane and exemestane (AROMASIN®), andnonsteroidal aromatase inhibitors such as anastrazole (ARIMIDEX®),letrozole (FEMARA®) and aminoglutethimide, and other aromataseinhibitors include vorozole (RIVISOR®), megestrol acetate (MEGASE®),fadrozole, and 4(5)-imidazoles; lutenizing hormone-releasing hormoneagonists, including leuprolide (LUPRON® and ELIGARD®), goserelin,buserelin, and tripterelin; sex steroids, including progestines such asmegestrol acetate and medroxyprogesterone acetate, estrogens such asdiethylstilbestrol and premarin, and androgens/retinoids such asfluoxymesterone, all transretionic acid and fenretinide; onapristone;anti-progesterones; estrogen receptor down-regulators (ERDs);anti-androgens such as flutamide, nilutamide and bicalutamide; andpharmaceutically acceptable salts, acids or derivatives of any of theabove; as well as combinations of two or more of the above.

A “growth inhibitory agent” when used herein refers to a compound orcomposition which inhibits growth of a cell (such as a cell expressingEGFL7) either in vitro or in vivo. Thus, the growth inhibitory agent maybe one which significantly reduces the percentage of cells (such as acell expressing EGFL7) in S phase. Examples of growth inhibitory agentsinclude agents that block cell cycle progression (at a place other thanS phase), such as agents that induce G1 arrest and M-phase arrest.Classical M-phase blockers include the vincas (vincristine andvinblastine), taxanes, and topoisomerase II inhibitors such asdoxorubicin, epirubicin, daunorubicin, etoposide, and bleomycin. Thoseagents that arrest G1 also spill over into S-phase arrest, for example,DNA alkylating agents such as tamoxifen, prednisone, dacarbazine,mechlorethamine, cisplatin, methotrexate, 5-fluorouracil, and ara-C.Further information can be found in Mendelsohn and Israel, eds., TheMolecular Basis of Cancer, Chapter 1, entitled “Cell cycle regulation,oncogenes, and antineoplastic drugs” by Murakami et al. (W.B. Saunders,Philadelphia, 1995), e.g., p. 13. The taxanes (paclitaxel and docetaxel)are anticancer drugs both derived from the yew tree. Docetaxel(TAXOTERE®, Rhone-Poulenc Rorer), derived from the European yew, is asemisynthetic analogue of paclitaxel (TAXOL®, Bristol-Myers Squibb).Paclitaxel and docetaxel promote the assembly of microtubules fromtubulin dimers and stabilize microtubules by preventingdepolymerization, which results in the inhibition of mitosis in cells.

“Doxorubicin” is an anthracycline antibiotic. The full chemical name ofdoxorubicin is(8S-cis)-10-[(3-amino-2,3,6-trideoxy-α-L-lyxo-hexapyranosyl)oxy]-7,8,9,10-tetrahydro-6,8,11-trihydroxy-8-(hydroxyacetyl)-1-methoxy-5,12-naphthacenedione.

The term “Fc region-comprising polypeptide” refers to a polypeptide,such as an antibody or immunoadhesin (see definitions below), whichcomprises an Fc region. The C-terminal lysine (residue 447 according tothe EU numbering system) of the Fc region may be removed, for example,during purification of the polypeptide or by recombinant engineering thenucleic acid encoding the polypeptide. Accordingly, a compositioncomprising a polypeptide having an Fc region according to this inventioncan comprise polypeptides with K447, with all K447 removed, or a mixtureof polypeptides with and without the K447 residue.

Throughout this specification and claims, the word “comprise,” orvariations such as “comprises” or “comprising,” will be understood toimply the inclusion of a stated integer or group of integers but not theexclusion of any other integer or group of integers.

Generating Variant Antibodies Exhibiting Reduced or Absence of HAMAResponse

Reduction or elimination of a HAMA response is a significant aspect ofclinical development of suitable therapeutic agents. See, e.g.,Khaxzaeli et al., J. Natl. Cancer Inst. (1988), 80:937; Jaffers et al.,Transplantation (1986), 41:572; Shawler et al., J. Immunol. (1985),135:1530; Sears et al., J. Biol. Response Mod. (1984), 3:138; Miller etal., Blood (1983), 62:988; Hakimi et al., J. Immunol. (1991), 147:1352;Reichmann et al., Nature (1988), 332:323; Junghans et al., Cancer Res.(1990), 50:1495. As described herein, the invention provides antibodiesthat are humanized such that HAMA response is reduced or eliminated.Variants of these antibodies can further be obtained using routinemethods known in the art, some of which are further described below.

For example, an amino acid sequence from an antibody as described hereincan serve as a starting (parent) sequence for diversification of theframework and/or hypervariable sequence(s). A selected frameworksequence to which a starting hypervariable sequence is linked isreferred to herein as an acceptor human framework. While the acceptorhuman frameworks may be from, or derived from, a human immunoglobulin(the VL and/or VH regions thereof), preferably the acceptor humanframeworks are from, or derived from, a human consensus frameworksequence as such frameworks have been demonstrated to have minimal, orno, immunogenicity in human patients.

Where the acceptor is derived from a human immunoglobulin, one mayoptionally select a human framework sequence that is selected based onits homology to the donor framework sequence by aligning the donorframework sequence with various human framework sequences in acollection of human framework sequences, and select the most homologousframework sequence as the acceptor.

In one embodiment, human consensus frameworks herein are from, orderived from, VH subgroup III and/or VL kappa subgroup I consensusframework sequences.

Thus, the VH acceptor human framework may comprise one, two, three orall of the following framework sequences:

(SEQ ID NO: 197) FR1 comprising EVQLVESGGGLVQPGGSLRLSCAAS,(SEQ ID NO: 198) FR2 comprising WVRQAPGKGLEWV, (SEQ ID NO: 205)FR3 comprising FR3 comprises RFTISX₁DX₂SKNTX₃YLQMNSLRAEDTAVYYC,wherein X₁ is A or R, X₂ is T or N, and X₃ is A or L, (SEQ ID NO: 200)FR4 comprising WGQGTLVTVSS.

In one embodiment, the VH acceptor human framework comprises one, two,three or all of the following framework sequences:

(SEQ ID NO: 197) FR1 comprising EVQLVESGGGLVQPGGSLRLSCAAS,(SEQ ID NO: 198) FR2 comprising WVRQAPGKGLEWV, (SEQ ID NO: 231)FR3 comprising RFTISADTSKNTAYLQMNSLRAEDTAVYYC, (SEQ ID NO: 206)RFTISADTSKNTAYLQMNSLRAEDTAVYYCA, (SEQ ID NO: 207)RFTISADTSKNTAYLQMNSLRAEDTAVYYCAR, (SEQ ID NO: 208)RFTISADTSKNTAYLQMNSLRAEDTAVYYCS, or (SEQ ID NO: 209)RFTISADTSKNTAYLQMNSLRAEDTAVYYCSR (SEQ ID NO: 200)FR4 comprising WGQGTLVTVSS.

The VL acceptor human framework may comprise one, two, three or all ofthe following framework sequences:

(SEQ ID NO: 201) FR1 comprising DIQMTQSPSSLSASVGDRVTITC,(SEQ ID NO: 202) FR2 comprising WYQQKPGKAPKLLIY, (SEQ ID NO: 203)FR3 comprising GVPSRFSGSGSGTDFTLTISSLQPEDFATYYC, (SEQ ID NO: 221)FR4 comprising FGQGTKVEIK.

While the acceptor may be identical in sequence to the human frameworksequence selected, whether that is from a human immunoglobulin or ahuman consensus framework, the present invention contemplates that theacceptor sequence may comprise pre-existing amino acid substitutionsrelative to the human immunoglobulin sequence or human consensusframework sequence. These pre-existing substitutions are preferablyminimal; usually four, three, two or one amino acid differences onlyrelative to the human immunoglobulin sequence or consensus frameworksequence.

Hypervariable region residues of the non-human antibody are incorporatedinto the VL and/or VH acceptor human frameworks. For example, one mayincorporate residues corresponding to the Kabat CDR residues, theChothia hypervariable loop residues, the Abm residues, and/or contactresidues. Optionally, the extended hypervariable region residues asfollows are incorporated: 24-34 (L1), 50-56 (L2) and 89-97 (L3), 26-35(H1), 50-65 or 49-65 (H2) and 93-102, 94-102, or 95-102 (H3).

While “incorporation” of hypervariable region residues is discussedherein, it will be appreciated that this can be achieved in variousways, for example, nucleic acid encoding the desired amino acid sequencecan be generated by mutating nucleic acid encoding the mouse variabledomain sequence so that the framework residues thereof are changed toacceptor human framework residues, or by mutating nucleic acid encodingthe human variable domain sequence so that the hypervariable domainresidues are changed to non-human residues, or by synthesizing nucleicacid encoding the desired sequence, etc.

In the examples herein, hypervariable region-grafted variants weregenerated by Kunkel mutagenesis of nucleic acid encoding the humanacceptor sequences, using a separate oligonucleotide for eachhypervariable region. Kunkel et al., Methods Enzymol. 154:367-382(1987). Appropriate changes can be introduced within the frameworkand/or hypervariable region, using routine techniques, to correct andre-establish proper hypervariable region-antigen interactions.

Phage(mid) display (also referred to herein as phage display in somecontexts) can be used as a convenient and fast method for generating andscreening many different potential variant antibodies in a librarygenerated by sequence randomization. However, other methods for makingand screening altered antibodies are available to the skilled person.

Phage(mid) display technology has provided a powerful tool forgenerating and selecting novel proteins which bind to a ligand, such asan antigen. Using the techniques of phage(mid) display allows thegeneration of large libraries of protein variants which can be rapidlysorted for those sequences that bind to a target molecule with highaffinity. Nucleic acids encoding variant polypeptides are generallyfused to a nucleic acid sequence encoding a viral coat protein, such asthe gene III protein or the gene VIII protein. Monovalent phagemiddisplay systems where the nucleic acid sequence encoding the protein orpolypeptide is fused to a nucleic acid sequence encoding a portion ofthe gene III protein have been developed. (Bass, S., Proteins, 8:309(1990); Lowman and Wells, Methods: A Companion to Methods in Enzymology,3:205 (1991)). In a monovalent phagemid display system, the gene fusionis expressed at low levels and wild type gene III proteins are alsoexpressed so that infectivity of the particles is retained. Methods ofgenerating peptide libraries and screening those libraries have beendisclosed in many patents (e.g. U.S. Pat. No. 5,723,286, U.S. Pat. No.5,432,018, U.S. Pat. No. 5,580,717, U.S. Pat. No. 5,427,908 and U.S.Pat. No. 5,498,530).

Libraries of antibodies or antigen binding polypeptides have beenprepared in a number of ways including by altering a single gene byinserting random DNA sequences or by cloning a family of related genes.Methods for displaying antibodies or antigen binding fragments usingphage(mid) display have been described in U.S. Pat. Nos. 5,750,373,5,733,743, 5,837,242, 5,969,108, 6,172,197, 5,580,717, and 5,658,727.The library is then screened for expression of antibodies or antigenbinding proteins with the desired characteristics.

Methods of substituting an amino acid of choice into a template nucleicacid are well established in the art, some of which are describedherein. For example, hypervariable region residues can be substitutedusing the Kunkel method. See, e.g., Kunkel et al., Methods Enzymol.154:367-382 (1987).

The sequence of oligonucleotides includes one or more of the designedcodon sets for the hypervariable region residues to be altered. A codonset is a set of different nucleotide triplet sequences used to encodedesired variant amino acids. Codon sets can be represented using symbolsto designate particular nucleotides or equimolar mixtures of nucleotidesas shown in below according to the IUB code.

IUB Codes

G Guanine

A Adenine

T Thymine

C Cytosine

R (A or G)

Y (C or T)

M (A or C)

K (G or T)

S(C or G)

W (A or T)

H (A or C or T)

B (C or G or T)

V (A or C or G)

D (A or G or T)

N (A or C or G or T)

For example, in the codon set DVK, D can be nucleotides A or G or T; Vcan be A or G or C; and K can be G or T. This codon set can present 18different codons and can encode amino acids Ala, Trp, Tyr, Lys, Thr,Asn, Lys, Ser, Arg, Asp, Glu, Gly, and Cys.

Oligonucleotide or primer sets can be synthesized using standardmethods. A set of oligonucleotides can be synthesized, for example, bysolid phase synthesis, containing sequences that represent all possiblecombinations of nucleotide triplets provided by the codon set and thatwill encode the desired group of amino acids. Synthesis ofoligonucleotides with selected nucleotide “degeneracy” at certainpositions is well known in that art. Such sets of nucleotides havingcertain codon sets can be synthesized using commercial nucleic acidsynthesizers (available from, for example, Applied Biosystems, FosterCity, Calif.), or can be obtained commercially (for example, from LifeTechnologies, Rockville, Md.). Therefore, a set of oligonucleotidessynthesized having a particular codon set will typically include aplurality of oligonucleotides with different sequences, the differencesestablished by the codon set within the overall sequence.Oligonucleotides, as used according to the invention, have sequencesthat allow for hybridization to a variable domain nucleic acid templateand also can include restriction enzyme sites for cloning purposes.

In one method, nucleic acid sequences encoding variant amino acids canbe created by oligonucleotide-mediated mutagenesis. This technique iswell known in the art as described by Zoller et al. Nucleic Acids Res.10:6487-6504 (1987). Briefly, nucleic acid sequences encoding variantamino acids are created by hybridizing an oligonucleotide set encodingthe desired codon sets to a DNA template, where the template is thesingle-stranded form of the plasmid containing a variable region nucleicacid template sequence. After hybridization, DNA polymerase is used tosynthesize an entire second complementary strand of the template thatwill thus incorporate the oligonucleotide primer, and will contain thecodon sets as provided by the oligonucleotide set.

Generally, oligonucleotides of at least 25 nucleotides in length areused. An optimal oligonucleotide will have 12 to 15 nucleotides that arecompletely complementary to the template on either side of thenucleotide(s) coding for the mutation(s). This ensures that theoligonucleotide will hybridize properly to the single-stranded DNAtemplate molecule. The oligonucleotides are readily synthesized usingtechniques known in the art such as that described by Crea et al., Proc.Nat'l. Acad. Sci. USA, 75:5765 (1978).

The DNA template is generated by those vectors that are either derivedfrom bacteriophage M13 vectors (the commercially available M13 mp18 andM13 mp19 vectors are suitable), or those vectors that contain asingle-stranded phage origin of replication as described by Viera etal., Meth. Enzymol., 153:3 (1987). Thus, the DNA that is to be mutatedcan be inserted into one of these vectors in order to generatesingle-stranded template. Production of the single-stranded template isdescribed in sections 4.21-4.41 of Sambrook et al., above.

To alter the native DNA sequence, the oligonucleotide is hybridized tothe single stranded template under suitable hybridization conditions. ADNA polymerizing enzyme, usually T7 DNA polymerase or the Klenowfragment of DNA polymerase I, is then added to synthesize thecomplementary strand of the template using the oligonucleotide as aprimer for synthesis. A heteroduplex molecule is thus formed such thatone strand of DNA encodes the mutated form of gene 1, and the otherstrand (the original template) encodes the native, unaltered sequence ofgene 1. This heteroduplex molecule is then transformed into a suitablehost cell, usually a prokaryote such as E. coli JM101. After growing thecells, they are plated onto agarose plates and screened using theoligonucleotide primer radiolabelled with a 32-Phosphate to identify thebacterial colonies that contain the mutated DNA.

The method described immediately above may be modified such that ahomoduplex molecule is created wherein both strands of the plasmidcontain the mutation(s). The modifications are as follows: The singlestranded oligonucleotide is annealed to the single-stranded template asdescribed above. A mixture of three deoxyribonucleotides,deoxyriboadenosine (dATP), deoxyriboguanosine (dGTP), anddeoxyribothymidine (dTT), is combined with a modifiedthiodeoxyribocytosine called dCTP-(aS) (which can be obtained fromAmersham). This mixture is added to the template-oligonucleotidecomplex. Upon addition of DNA polymerase to this mixture, a strand ofDNA identical to the template except for the mutated bases is generated.In addition, this new strand of DNA will contain dCTP-(aS) instead ofdCTP, which serves to protect it from restriction endonucleasedigestion. After the template strand of the double-stranded heteroduplexis nicked with an appropriate restriction enzyme, the template strandcan be digested with ExoIII nuclease or another appropriate nucleasepast the region that contains the site(s) to be mutagenized. Thereaction is then stopped to leave a molecule that is only partiallysingle-stranded. A complete double-stranded DNA homoduplex is thenformed using DNA polymerase in the presence of all fourdeoxyribonucleotide triphosphates, ATP, and DNA ligase. This homoduplexmolecule can then be transformed into a suitable host cell.

As indicated previously the sequence of the oligonucleotide set is ofsufficient length to hybridize to the template nucleic acid and mayalso, but does not necessarily, contain restriction sites. The DNAtemplate can be generated by those vectors that are either derived frombacteriophage M13 vectors or vectors that contain a single-strandedphage origin of replication as described by Viera et al. Meth. Enzymol.,153:3 (1987). Thus, the DNA that is to be mutated must be inserted intoone of these vectors in order to generate single-stranded template.Production of the single-stranded template is described in sections4.21-4.41 of Sambrook et al., supra.

According to another method, a library can be generated by providingupstream and downstream oligonucleotide sets, each set having aplurality of oligonucleotides with different sequences, the differentsequences established by the codon sets provided within the sequence ofthe oligonucleotides. The upstream and downstream oligonucleotide sets,along with a variable domain template nucleic acid sequence, can be usedin a polymerase chain reaction to generate a “library” of PCR products.The PCR products can be referred to as “nucleic acid cassettes”, as theycan be fused with other related or unrelated nucleic acid sequences, forexample, viral coat proteins and dimerization domains, using establishedmolecular biology techniques.

The sequence of the PCR primers includes one or more of the designedcodon sets for the solvent accessible and highly diverse positions in ahypervariable region. As described above, a codon set is a set ofdifferent nucleotide triplet sequences used to encode desired variantamino acids.

Antibody selectants that meet the desired criteria, as selected throughappropriate screening/selection steps can be isolated and cloned usingstandard recombinant techniques.

Antibody Fragments

The present invention encompasses antibody fragments. Antibody fragmentsmay be generated by traditional means, such as enzymatic digestion, orby recombinant techniques. In certain circumstances there are advantagesof using antibody fragments, rather than whole antibodies. The smallersize of the fragments allows for rapid clearance, and may lead toimproved access to solid tumors. For a review of certain antibodyfragments, see Hudson et al. (2003) Nat. Med. 9:129-134.

Various techniques have been developed for the production of antibodyfragments. Traditionally, these fragments were derived via proteolyticdigestion of intact antibodies (see, e.g., Morimoto et al., Journal ofBiochemical and Biophysical Methods 24:107-117 (1992); and Brennan etal., Science, 229:81 (1985)). However, these fragments can now beproduced directly by recombinant host cells. Fab, Fv and ScFv antibodyfragments can all be expressed in and secreted from E. coli, thusallowing the facile production of large amounts of these fragments.Antibody fragments can be isolated from the antibody phage librariesdiscussed above. Alternatively, Fab′-SH fragments can be directlyrecovered from E. coli and chemically coupled to form F(ab′)₂ fragments(Carter et al., Bio/Technology 10:163-167 (1992)). According to anotherapproach, F(ab′)₂ fragments can be isolated directly from recombinanthost cell culture. Fab and F(ab′)₂ fragment with increased in vivohalf-life comprising salvage receptor binding epitope residues aredescribed in U.S. Pat. No. 5,869,046. Other techniques for theproduction of antibody fragments will be apparent to the skilledpractitioner. In certain embodiments, an antibody is a single chain Fvfragment (scFv). See WO 93/16185; U.S. Pat. Nos. 5,571,894; and5,587,458. Fv and scFv are the only species with intact combining sitesthat are devoid of constant regions; thus, they may be suitable forreduced nonspecific binding during in vivo use. scFv fusion proteins maybe constructed to yield fusion of an effector protein at either theamino or the carboxy terminus of an scFv. See Antibody Engineering, ed.Borrebaeck, supra. The antibody fragment may also be a “linearantibody”, e.g., as described in U.S. Pat. No. 5,641,870, for example.Such linear antibodies may be monospecific or bispecific.

Humanized Antibodies

The invention encompasses humanized antibodies. Various methods forhumanizing non-human antibodies are known in the art. For example, ahumanized antibody can have one or more amino acid residues introducedinto it from a source which is non-human. These non-human amino acidresidues are often referred to as “import” residues, which are typicallytaken from an “import” variable domain. Humanization can be essentiallyperformed following the method of Winter and co-workers (Jones et al.(1986) Nature 321:522-525; Riechmann et al. (1988) Nature 332:323-327;Verhoeyen et al. (1988) Science 239:1534-1536), by substitutinghypervariable region sequences for the corresponding sequences of ahuman antibody. Accordingly, such “humanized” antibodies are chimericantibodies (U.S. Pat. No. 4,816,567) wherein substantially less than anintact human variable domain has been substituted by the correspondingsequence from a non-human species. In practice, humanized antibodies aretypically human antibodies in which some hypervariable region residuesand possibly some FR residues are substituted by residues from analogoussites in rodent antibodies.

The choice of human variable domains, both light and heavy, to be usedin making the humanized antibodies can be important to reduceantigenicity. According to the so-called “best-fit” method, the sequenceof the variable domain of a rodent antibody is screened against theentire library of known human variable-domain sequences. The humansequence which is closest to that of the rodent is then accepted as thehuman framework for the humanized antibody. See, e.g., Sims et al.(1993) J. Immunol. 151:2296; Chothia et al. (1987) J. Mol. Biol.196:901. Another method uses a particular framework derived from theconsensus sequence of all human antibodies of a particular subgroup oflight or heavy chains. The same framework may be used for severaldifferent humanized antibodies. See, e.g., Carter et al. (1992) Proc.Natl. Acad. Sci. USA, 89:4285; Presta et al. (1993) J. Immunol.,151:2623.

It is further generally desirable that antibodies be humanized withretention of high affinity for the antigen and other favorablebiological properties. To achieve this goal, according to one method,humanized antibodies are prepared by a process of analysis of theparental sequences and various conceptual humanized products usingthree-dimensional models of the parental and humanized sequences.Three-dimensional immunoglobulin models are commonly available and arefamiliar to those skilled in the art. Computer programs are availablewhich illustrate and display probable three-dimensional conformationalstructures of selected candidate immunoglobulin sequences. Inspection ofthese displays permits analysis of the likely role of the residues inthe functioning of the candidate immunoglobulin sequence, i.e., theanalysis of residues that influence the ability of the candidateimmunoglobulin to bind its antigen. In this way, FR residues can beselected and combined from the recipient and import sequences so thatthe desired antibody characteristic, such as increased affinity for thetarget antigen(s), is achieved. In general, the hypervariable regionresidues are directly and most substantially involved in influencingantigen binding.

Human Antibodies

Human antibodies of the invention can be constructed by combining Fvclone variable domain sequence(s) selected from human-derived phagedisplay libraries with known human constant domain sequences(s) asdescribed above. Alternatively, human monoclonal antibodies of theinvention can be made by the hybridoma method. Human myeloma andmouse-human heteromyeloma cell lines for the production of humanmonoclonal antibodies have been described, for example, by Kozbor J.Immunol., 133: 3001 (1984); Brodeur et al., Monoclonal AntibodyProduction Techniques and Applications, pp. 51-63 (Marcel Dekker, Inc.,New York, 1987); and Boerner et al., J. Immunol., 147: 86 (1991).

It is now possible to produce transgenic animals (e.g. mice) that arecapable, upon immunization, of producing a full repertoire of humanantibodies in the absence of endogenous immunoglobulin production. Forexample, it has been described that the homozygous deletion of theantibody heavy-chain joining region (JH) gene in chimeric and germ-linemutant mice results in complete inhibition of endogenous antibodyproduction. Transfer of the human germ-line immunoglobulin gene array insuch germ-line mutant mice will result in the production of humanantibodies upon antigen challenge. See, e.g., Jakobovits et al., Proc.Natl. Acad. Sci. USA, 90: 2551 (1993); Jakobovits et al., Nature, 362:255 (1993); Bruggermann et al., Year in Immunol., 7: 33 (1993).

Gene shuffling can also be used to derive human antibodies fromnon-human, e.g. rodent, antibodies, where the human antibody has similaraffinities and specificities to the starting non-human antibody.According to this method, which is also called “epitope imprinting”,either the heavy or light chain variable region of a non-human antibodyfragment obtained by phage display techniques as described herein isreplaced with a repertoire of human V domain genes, creating apopulation of non-human chain/human chain scFv or Fab chimeras.Selection with antigen results in isolation of a non-human chain/humanchain chimeric scFv or Fab wherein the human chain restores the antigenbinding site destroyed upon removal of the corresponding non-human chainin the primary phage display clone, i.e. the epitope governs (imprints)the choice of the human chain partner. When the process is repeated inorder to replace the remaining non-human chain, a human antibody isobtained (see PCT WO 93/06213 published Apr. 1, 1993). Unliketraditional humanization of non-human antibodies by HVR grafting, thistechnique provides completely human antibodies, which have no FR or HVRresidues of non-human origin.

Bispecific Antibodies

Bispecific antibodies are monoclonal antibodies that have bindingspecificities for at least two different antigens. In certainembodiments, bispecific antibodies are human or humanized antibodies. Incertain embodiments, one of the binding specificities is for EGFL7 andthe other is for any other antigen. In certain embodiments, the otherantigen is vascular endothelial growth factor (VEGF), e.g. the epitopebound by the antibodies bevacizumab and ranibizumab. In certainembodiments, the bispecific antibody has a first arm comprising the HVRsequences of an antibody of the invention and a second arm comprisingthe HVR sequences of bevacizumab or ranibizumab. In certain embodiments,the bispecific antibody comprises the VH and VL sequences of bevacizumabor ranibizumab. In certain embodiments, bispecific antibodies may bindto two different epitopes of EGFL7. Bispecific antibodies may also beused to localize cytotoxic agents to cells which express EGFL7. Theseantibodies possess a EGFL7-binding arm and an arm which binds acytotoxic agent, such as, e.g., saporin, anti-interferon-α, vincaalkaloid, ricin A chain, methotrexate or radioactive isotope hapten.Bispecific antibodies can be prepared as full length antibodies orantibody fragments (e.g. F(ab′)₂ bispecific antibodies).

Methods for making bispecific antibodies are known in the art.Traditionally, the recombinant production of bispecific antibodies isbased on the co-expression of two immunoglobulin heavy chain-light chainpairs, where the two heavy chains have different specificities (Milsteinand Cuello, Nature, 305: 537 (1983)). Because of the random assortmentof immunoglobulin heavy and light chains, these hybridomas (quadromas)produce a potential mixture of 10 different antibody molecules, of whichonly one has the correct bispecific structure. The purification of thecorrect molecule, which is usually done by affinity chromatographysteps, is rather cumbersome, and the product yields are low. Similarprocedures are disclosed in WO 93/08829 published May 13, 1993, and inTraunecker et al., EMBO J., 10: 3655 (1991).

According to a different approach, antibody variable domains with thedesired binding specificities (antibody-antigen combining sites) arefused to immunoglobulin constant domain sequences. The fusion, forexample, is with an immunoglobulin heavy chain constant domain,comprising at least part of the hinge, CH2, and CH3 regions. In certainembodiments, the first heavy-chain constant region (CH1), containing thesite necessary for light chain binding, is present in at least one ofthe fusions. DNAs encoding the immunoglobulin heavy chain fusions and,if desired, the immunoglobulin light chain, are inserted into separateexpression vectors, and are co-transfected into a suitable hostorganism. This provides for great flexibility in adjusting the mutualproportions of the three polypeptide fragments in embodiments whenunequal ratios of the three polypeptide chains used in the constructionprovide the optimum yields. It is, however, possible to insert thecoding sequences for two or all three polypeptide chains in oneexpression vector when the expression of at least two polypeptide chainsin equal ratios results in high yields or when the ratios are of noparticular significance.

In one embodiment of this approach, the bispecific antibodies arecomposed of a hybrid immunoglobulin heavy chain with a first bindingspecificity in one arm, and a hybrid immunoglobulin heavy chain-lightchain pair (providing a second binding specificity) in the other arm. Itwas found that this asymmetric structure facilitates the separation ofthe desired bispecific compound from unwanted immunoglobulin chaincombinations, as the presence of an immunoglobulin light chain in onlyone half of the bispecific molecule provides for a facile way ofseparation. This approach is disclosed in WO 94/04690. For furtherdetails of generating bispecific antibodies see, for example, Suresh etal., Methods in Enzymology, 121:210 (1986).

According to another approach, the interface between a pair of antibodymolecules can be engineered to maximize the percentage of heterodimerswhich are recovered from recombinant cell culture. The interfacecomprises at least a part of the CH3 domain of an antibody constantdomain. In this method, one or more small amino acid side chains fromthe interface of the first antibody molecule are replaced with largerside chains (e.g. tyrosine or tryptophan). Compensatory “cavities” ofidentical or similar size to the large side chain(s) are created on theinterface of the second antibody molecule by replacing large amino acidside chains with smaller ones (e.g. alanine or threonine). This providesa mechanism for increasing the yield of the heterodimer over otherunwanted end-products such as homodimers.

Bispecific antibodies include cross-linked or “heteroconjugate”antibodies. For example, one of the antibodies in the heteroconjugatecan be coupled to avidin, the other to biotin. Such antibodies have, forexample, been proposed to target immune system cells to unwanted cells(U.S. Pat. No. 4,676,980), and for treatment of HIV infection (WO91/00360, WO 92/00373, and EP 03089). Heteroconjugate antibodies may bemade using any convenient cross-linking method. Suitable cross-linkingagents are well known in the art, and are disclosed in U.S. Pat. No.4,676,980, along with a number of cross-linking techniques.

Techniques for generating bispecific antibodies from antibody fragmentshave also been described in the literature. For example, bispecificantibodies can be prepared using chemical linkage. Brennan et al.,Science, 229: 81 (1985) describe a procedure wherein intact antibodiesare proteolytically cleaved to generate F(ab′)₂ fragments. Thesefragments are reduced in the presence of the dithiol complexing agentsodium arsenite to stabilize vicinal dithiols and prevent intermoleculardisulfide formation. The Fab′ fragments generated are then converted tothionitrobenzoate (TNB) derivatives. One of the Fab′-TNB derivatives isthen reconverted to the Fab′-thiol by reduction with mercaptoethylamineand is mixed with an equimolar amount of the other Fab′-TNB derivativeto form the bispecific antibody. The bispecific antibodies produced canbe used as agents for the selective immobilization of enzymes.

Recent progress has facilitated the direct recovery of Fab′-SH fragmentsfrom E. coli, which can be chemically coupled to form bispecificantibodies. Shalaby et al., J. Exp. Med., 175: 217-225 (1992) describethe production of a fully humanized bispecific antibody F(ab′)₂molecule. Each Fab′ fragment was separately secreted from E. coli andsubjected to directed chemical coupling in vitro to form the bispecificantibody. The bispecific antibody thus formed was able to bind to cellsoverexpressing the HER2 receptor and normal human T cells, as well astrigger the lytic activity of human cytotoxic lymphocytes against humanbreast tumor targets.

Various techniques for making and isolating bispecific antibodyfragments directly from recombinant cell culture have also beendescribed. For example, bispecific antibodies have been produced usingleucine zippers. Kostelny et al., J. Immunol., 148(5):1547-1553 (1992).The leucine zipper peptides from the Fos and Jun proteins were linked tothe Fab′ portions of two different antibodies by gene fusion. Theantibody homodimers were reduced at the hinge region to form monomersand then re-oxidized to form the antibody heterodimers. This method canalso be utilized for the production of antibody homodimers. The“diabody” technology described by Hollinger et al., Proc. Natl. Acad.Sci. USA, 90:6444-6448 (1993) has provided an alternative mechanism formaking bispecific antibody fragments. The fragments comprise aheavy-chain variable domain (VH) connected to a light-chain variabledomain (VL) by a linker which is too short to allow pairing between thetwo domains on the same chain. Accordingly, the VH and VL domains of onefragment are forced to pair with the complementary VL and VH domains ofanother fragment, thereby forming two antigen-binding sites. Anotherstrategy for making bispecific antibody fragments by the use ofsingle-chain Fv (sFv) dimers has also been reported. See Gruber et al.,J. Immunol., 152:5368 (1994).

Antibodies with more than two valencies are contemplated. For example,trispecific antibodies can be prepared. Tutt et al. J. Immunol. 147: 60(1991).

Multivalent Antibodies

A multivalent antibody may be internalized (and/or catabolized) fasterthan a bivalent antibody by a cell expressing an antigen to which theantibodies bind. The antibodies of the present invention can bemultivalent antibodies (which are other than of the IgM class) withthree or more antigen binding sites (e.g. tetravalent antibodies), whichcan be readily produced by recombinant expression of nucleic acidencoding the polypeptide chains of the antibody. The multivalentantibody can comprise a dimerization domain and three or more antigenbinding sites. In certain embodiments, the dimerization domain comprises(or consists of) an Fc region or a hinge region. In this scenario, theantibody will comprise an Fc region and three or more antigen bindingsites amino-terminal to the Fc region. In certain embodiments, amultivalent antibody comprises (or consists of) three to about eightantigen binding sites. In one such embodiment, a multivalent antibodycomprises (or consists of) four antigen binding sites. The multivalentantibody comprises at least one polypeptide chain (for example, twopolypeptide chains), wherein the polypeptide chain(s) comprise two ormore variable domains. For instance, the polypeptide chain(s) maycomprise VD1-(X1)n-VD2-(X2)n-Fc, wherein VD1 is a first variable domain,VD2 is a second variable domain, Fc is one polypeptide chain of an Fcregion, X1 and X2 represent an amino acid or polypeptide, and n is 0or 1. For instance, the polypeptide chain(s) may comprise:VH-CH1-flexible linker-VH-CH1-Fc region chain; or VH-CH1-VH-CH1-Fcregion chain. The multivalent antibody herein may further comprise atleast two (for example, four) light chain variable domain polypeptides.The multivalent antibody herein may, for instance, comprise from abouttwo to about eight light chain variable domain polypeptides. The lightchain variable domain polypeptides contemplated here comprise a lightchain variable domain and, optionally, further comprise a CL domain.

Single-Domain Antibodies

In some embodiments, an antibody of the invention is a single-domainantibody. A single-domain antibody is a single polyeptide chaincomprising all or a portion of the heavy chain variable domain or all ora portion of the light chain variable domain of an antibody. In certainembodiments, a single-domain antibody is a human single-domain antibody(Domantis, Inc., Waltham, Mass.; see, e.g., U.S. Pat. No. 6,248,516 B1).In one embodiment, a single-domain antibody consists of all or a portionof the heavy chain variable domain of an antibody.

Antibody Variants

In some embodiments, amino acid sequence modification(s) of theantibodies described herein are contemplated. For example, it may bedesirable to improve the binding affinity and/or other biologicalproperties of the antibody. Amino acid sequence variants of the antibodymay be prepared by introducing appropriate changes into the nucleotidesequence encoding the antibody, or by peptide synthesis. Suchmodifications include, for example, deletions from, and/or insertionsinto and/or substitutions of, residues within the amino acid sequencesof the antibody. Any combination of deletion, insertion, andsubstitution can be made to arrive at the final construct, provided thatthe final construct possesses the desired characteristics. The aminoacid alterations may be introduced in the subject antibody amino acidsequence at the time that sequence is made.

A useful method for identification of certain residues or regions of theantibody that are preferred locations for mutagenesis is called “alaninescanning mutagenesis” as described by Cunningham and Wells (1989)Science, 244:1081-1085. Here, a residue or group of target residues areidentified (e.g., charged residues such as arg, asp, his, lys, and glu)and replaced by a neutral or negatively charged amino acid (e.g.,alanine or polyalanine) to affect the interaction of the amino acidswith antigen. Those amino acid locations demonstrating functionalsensitivity to the substitutions then are refined by introducing furtheror other variants at, or for, the sites of substitution. Thus, while thesite for introducing an amino acid sequence variation is predetermined,the nature of the mutation per se need not be predetermined. Forexample, to analyze the performance of a mutation at a given site, alascanning or random mutagenesis is conducted at the target codon orregion and the expressed immunoglobulins are screened for the desiredactivity.

Amino acid sequence insertions include amino- and/or carboxyl-terminalfusions ranging in length from one residue to polypeptides containing ahundred or more residues, as well as intrasequence insertions of singleor multiple amino acid residues. Examples of terminal insertions includean antibody with an N-terminal methionyl residue. Other insertionalvariants of the antibody molecule include the fusion to the N- orC-terminus of the antibody to an enzyme (e.g. for ADEPT) or apolypeptide which increases the serum half-life of the antibody.

In certain embodiments, an antibody of the invention is altered toincrease or decrease the extent to which the antibody is glycosylated.Glycosylation of polypeptides is typically either N-linked or O-linked.N-linked refers to the attachment of a carbohydrate moiety to the sidechain of an asparagine residue. The tripeptide sequencesasparagine-X-serine and asparagine-X-threonine, where X is any aminoacid except proline, are the recognition sequences for enzymaticattachment of the carbohydrate moiety to the asparagine side chain.Thus, the presence of either of these tripeptide sequences in apolypeptide creates a potential glycosylation site. O-linkedglycosylation refers to the attachment of one of the sugarsN-aceylgalactosamine, galactose, or xylose to a hydroxyamino acid, mostcommonly serine or threonine, although 5-hydroxyproline or5-hydroxylysine may also be used.

Addition or deletion of glycosylation sites to the antibody isconveniently accomplished by altering the amino acid sequence such thatone or more of the above-described tripeptide sequences (for N-linkedglycosylation sites) is created or removed. The alteration may also bemade by the addition, deletion, or substitution of one or more serine orthreonine residues to the sequence of the original antibody (forO-linked glycosylation sites).

Where the antibody comprises an Fc region, the carbohydrate attachedthereto may be altered. Native antibodies produced by mammalian cellstypically comprise a branched, biantennary oligosaccharide that isgenerally attached by an N-linkage to Asn297 of the CH2 domain of the Fcregion. See, e.g., Wright et al. (1997) TIBTECH 15:26-32. Theoligosaccharide may include various carbohydrates, e.g., mannose,N-acetyl glucosamine (GlcNAc), galactose, and sialic acid, as well as afucose attached to a GlcNAc in the “stem” of the biantennaryoligosaccharide structure. In some embodiments, modifications of theoligosaccharide in an antibody of the invention may be made in order tocreate antibody variants with certain improved properties.

For example, antibody variants are provided having a carbohydratestructure that lacks fucose attached (directly or indirectly) to an Fcregion. Such variants may have improved ADCC function. See, e.g., USPatent Publication Nos. US 2003/0157108 (Presta, L.); US 2004/0093621(Kyowa Hakko Kogyo Co., Ltd). Examples of publications related to“defucosylated” or “fucose-deficient” antibody variants include: US2003/0157108; WO 2000/61739; WO 2001/29246; US 2003/0115614; US2002/0164328; US 2004/0093621; US 2004/0132140; US 2004/0110704; US2004/0110282; US 2004/0109865; WO 2003/085119; WO 2003/084570; WO2005/035586; WO 2005/035778; WO2005/053742; WO2002/031140; Okazaki etal. J. Mol. Biol. 336:1239-1249 (2004); Yamane-Ohnuki et al. Biotech.Bioeng. 87: 614 (2004). Examples of cell lines capable of producingdefucosylated antibodies include Lec13 CHO cells deficient in proteinfucosylation (Ripka et al. Arch. Biochem. Biophys. 249:533-545 (1986);US Pat Appl No US 2003/0157108 A1, Presta, L; and WO 2004/056312 A1,Adams et al., especially at Example 11), and knockout cell lines, suchas alpha-1,6-fucosyltransferase gene, FUT8, knockout CHO cells (see,e.g., Yamane-Ohnuki et al. Biotech. Bioeng. 87: 614 (2004); Kanda, Y. etal., Biotechnol. Bioeng., 94(4):680-688 (2006); and WO2003/085107).

Antibodies variants are further provided with bisected oligosaccharides,e.g., in which a biantennary oligosaccharide attached to the Fc regionof the antibody is bisected by GlcNAc. Such antibody variants may havereduced fucosylation and/or improved ADCC function. Examples of suchantibody variants are described, e.g., in WO 2003/011878 (Jean-Mairet etal.); U.S. Pat. No. 6,602,684 (Umana et al.); and US 2005/0123546 (Umanaet al.). Antibody variants with at least one galactose residue in theoligosaccharide attached to the Fc region are also provided. Suchantibody variants may have improved CDC function. Such antibody variantsare described, e.g., in WO 1997/30087 (Patel et al.); WO 1998/58964(Raju, S.); and WO 1999/22764 (Raju, S.).

In certain embodiments, an antibody variant comprises an Fc region withone or more amino acid substitutions which further improve ADCC, forexample, substitutions at positions 298, 333, and/or 334 of the Fcregion (Eu numbering of residues). Such substitutions may occur incombination with any of the variations described above.

In certain embodiments, the invention contemplates an antibody variantthat possesses some but not all effector functions, which make it adesirable candidate for many applications in which the half life of theantibody in vivo is important yet certain effector functions (such ascomplement and ADCC) are unnecessary or deleterious. In certainembodiments, the Fc activities of the antibody are measured to ensurethat only the desired properties are maintained. In vitro and/or in vivocytotoxicity assays can be conducted to confirm the reduction/depletionof CDC and/or ADCC activities. For example, Fc receptor (FcR) bindingassays can be conducted to ensure that the antibody lacks FcγR binding(hence likely lacking ADCC activity), but retains FcRn binding ability.The primary cells for mediating ADCC, NK cells, express FcγRIII only,whereas monocytes express FcγRI, FcγRII and FcγRIII. FcR expression onhematopoietic cells is summarized in Table 3 on page 464 of Ravetch andKinet, Annu. Rev. Immunol. 9:457-92 (1991). Non-limiting examples of invitro assays to assess ADCC activity of a molecule of interest isdescribed in U.S. Pat. No. 5,500,362 (see, e.g. Hellstrom, I., et al.Proc. Nat'l Acad. Sci. USA 83:7059-7063 (1986)) and Hellstrom, I et al.,Proc. Nat'l Acad. Sci. USA 82:1499-1502 (1985); U.S. Pat. No. 5,821,337(see Bruggemann, M. et al., J. Exp. Med. 166:1351-1361 (1987)).Alternatively, non-radioactive assays methods may be employed (see, forexample, ACTI™ non-radioactive cytotoxicity assay for flow cytometry(CellTechnology, Inc. Mountain View, Calif.; and CytoTox 96®non-radioactive cytotoxicity assay (Promega, Madison, Wis.). Usefuleffector cells for such assays include peripheral blood mononuclearcells (PBMC) and Natural Killer (NK) cells. Alternatively, oradditionally, ADCC activity of the molecule of interest may be assessedin vivo, e.g., in a animal model such as that disclosed in Clynes et al.Proc. Nat'l Acad. Sci. USA 95:652-656 (1998). Clq binding assays mayalso be carried out to confirm that the antibody is unable to bind Clqand hence lacks CDC activity. To assess complement activation, a CDCassay may be performed (see, for example, Gazzano-Santoro et al., J.Immunol. Methods 202:163 (1996); Cragg, M. S. et al., Blood101:1045-1052 (2003); and Cragg, M. S. and M. J. Glennie, Blood103:2738-2743 (2004)). FcRn binding and in vivo clearance/half lifedeterminations can also be performed using methods known in the art(see, for example, Petkova, S. B. et al., Int'l. Immunol.18(12):1759-1769 (2006)).

Other antibody variants having one or more amino acid substitutions areprovided. Sites of interest for substitutional mutagenesis include thehypervariable regions, but FR alterations are also contemplated.Conservative substitutions are shown in Table 1 under the heading of“preferred substitutions.” More substantial changes, denominated“exemplary substitutions” are provided in the “Amino Acid SubstitutionTable”, or as further described below in reference to amino acidclasses. Amino acid substitutions may be introduced into an antibody ofinterest and the products screened, e.g., for a desired activity, suchas improved antigen binding, decreased immunogenicity, improved ADCC orCDC, etc.

Amino Acid Substitution Table Original Exemplary Preferred ResidueSubstitutions Substitutions Ala (A) Val; Leu; Ile Val Arg (R) Lys; Gln;Asn Lys Asn (N) Gln; His; Asp, Lys; Arg Gln Asp (D) Glu; Asn Glu Cys (C)Ser; Ala Ser Gln (Q) Asn; Glu Asn Glu (E) Asp; Gln Asp Gly (G) Ala AlaHis (H) Asn; Gln; Lys; Arg Arg Ile (I) Leu; Val; Met; Ala; Leu Phe;Norleucine Leu (L) Norleucine; Ile; Val; Ile Met; Ala; Phe Lys (K) Arg;Gln; Asn Arg Met (M) Leu; Phe; Ile Leu Phe (F) Trp; Leu; Val; Ile; Ala;Tyr Tyr Pro (P) Ala Ala Ser (S) Thr Thr Thr (T) Val; Ser Ser Trp (W)Tyr; Phe Tyr Tyr (Y) Trp; Phe; Thr; Ser Phe Val (V) Ile; Leu; Met; Phe;Leu Ala; Norleucine

Modifications in the biological properties of an antibody may beaccomplished by selecting substitutions that affect (a) the structure ofthe polypeptide backbone in the area of the substitution, for example,as a sheet or helical conformation, (b) the charge or hydrophobicity ofthe molecule at the target site, or (c) the bulk of the side chain.Amino acids may be grouped according to similarities in the propertiesof their side chains (in A. L. Lehninger, in Biochemistry, second ed.,pp. 73-75, Worth Publishers, New York (1975)):

(1) non-polar: Ala (A), Val (V), Leu (L), Ile (I), Pro (P), Phe (F), Trp(W), Met (M)

(2) uncharged polar: Gly (G), Ser (S), Thr (T), Cys (C), Tyr (Y), Asn(N), Gln (Q)

(3) acidic: Asp (D), Glu (E)

(4) basic: Lys (K), Arg (R), His (H)

Alternatively, naturally occurring residues may be divided into groupsbased on common side-chain properties:

(1) hydrophobic: Norleucine, Met, Ala, Val, Leu, Ile;

(2) neutral hydrophilic: Cys, Ser, Thr, Asn, Gln;

(3) acidic: Asp, Glu;

(4) basic: His, Lys, Arg;

(5) residues that influence chain orientation: Gly, Pro;

(6) aromatic: Trp, Tyr, Phe.

Non-conservative substitutions will entail exchanging a member of one ofthese classes for another class. Such substituted residues also may beintroduced into the conservative substitution sites or, into theremaining (non-conserved) sites.

One type of substitutional variant involves substituting one or morehypervariable region residues of a parent antibody (e.g. a humanized orhuman antibody). Generally, the resulting variant(s) selected forfurther development will have modified (e.g., improved) biologicalproperties relative to the parent antibody from which they aregenerated. An exemplary substitutional variant is an affinity maturedantibody, which may be conveniently generated using phage display-basedaffinity maturation techniques. Briefly, several hypervariable regionsites (e.g. 6-7 sites) are mutated to generate all possible amino acidsubstitutions at each site. The antibodies thus generated are displayedfrom filamentous phage particles as fusions to at least part of a phagecoat protein (e.g., the gene III product of M13) packaged within eachparticle. The phage-displayed variants are then screened for theirbiological activity (e.g. binding affinity). In order to identifycandidate hypervariable region sites for modification, scanningmutagenesis (e.g., alanine scanning) can be performed to identifyhypervariable region residues contributing significantly to antigenbinding. Alternatively, or additionally, it may be beneficial to analyzea crystal structure of the antigen-antibody complex to identify contactpoints between the antibody and antigen.

Such contact residues and neighboring residues are candidates forsubstitution according to techniques known in the art, including thoseelaborated herein. Once such variants are generated, the panel ofvariants is subjected to screening using techniques known in the art,including those described herein, and variants with superior propertiesin one or more relevant assays may be selected for further development.

Nucleic acid molecules encoding amino acid sequence variants of theantibody are prepared by a variety of methods known in the art. Thesemethods include, but are not limited to, isolation from a natural source(in the case of naturally occurring amino acid sequence variants) orpreparation by oligonucleotide-mediated (or site-directed) mutagenesis,PCR mutagenesis, and cassette mutagenesis of an earlier prepared variantor a non-variant version of the antibody.

It may be desirable to introduce one or more amino acid modifications inan Fc region of antibodies of the invention, thereby generating an Fcregion variant. The Fc region variant may comprise a human Fc regionsequence (e.g., a human IgG1, IgG2, IgG3 or IgG4 Fc region) comprisingan amino acid modification (e.g. a substitution) at one or more aminoacid positions including that of a hinge cysteine.

In accordance with this description and the teachings of the art, it iscontemplated that in some embodiments, an antibody of the invention maycomprise one or more alterations as compared to the wild typecounterpart antibody, e.g. in the Fc region. These antibodies wouldnonetheless retain substantially the same characteristics required fortherapeutic utility as compared to their wild type counterpart. Forexample, it is thought that certain alterations can be made in the Fcregion that would result in altered (i.e., either improved ordiminished) Clq binding and/or Complement Dependent Cytotoxicity (CDC),e.g., as described in WO99/51642. See also Duncan & Winter, Nature322:738-40 (1988); U.S. Pat. No. 5,648,260; U.S. Pat. No. 5,624,821; andWO94/29351 concerning other examples of Fc region variants. WO00/42072(Presta) and WO 2004/056312 (Lowman) describe antibody variants withimproved or diminished binding to FcRs. See, also, Shields et al. J.Biol. Chem. 9(2): 6591-6604 (2001). Antibodies with increased half livesand improved binding to the neonatal Fc receptor (FcRn), which isresponsible for the transfer of maternal IgGs to the fetus (Guyer etal., J. Immunol. 117:587 (1976) and Kim et al., J. Immunol. 24:249(1994)), are described in US2005/0014934A1 (Hinton et al.). Theseantibodies comprise an Fc region with one or more substitutions thereinwhich improve binding of the Fc region to FcRn. Polypeptide variantswith altered Fc region amino acid sequences and increased or decreasedClq binding capability are described in U.S. Pat. No. 6,194,551B1,WO99/51642. See, also, Idusogie et al. J. Immunol. 164: 4178-4184(2000).

In another aspect, the invention provides antibodies comprisingmodifications in the interface of Fc polypeptides comprising the Fcregion, wherein the modifications facilitate and/or promoteheterodimerization. These modifications comprise introduction of aprotuberance into a first Fc polypeptide and a cavity into a second Fcpolypeptide, wherein the protuberance is positionable in the cavity soas to promote complexing of the first and second Fc polypeptides.Methods of generating antibodies with these modifications are known inthe art, e.g., as described in U.S. Pat. No. 5,731,168.

In yet another aspect, it may be desirable to create cysteine engineeredantibodies, e.g., “thioMAbs,” in which one or more residues of anantibody are substituted with cysteine residues. In particularembodiments, the substituted residues occur at accessible sites of theantibody. By substituting those residues with cysteine, reactive thiolgroups are thereby positioned at accessible sites of the antibody andmay be used to conjugate the antibody to other moieties, such as drugmoieties or linker-drug moieties, as described further herein. Incertain embodiments, any one or more of the following residues may besubstituted with cysteine: V205 (Kabat numbering) of the light chain;A118 (EU numbering) of the heavy chain; and S400 (EU numbering) of theheavy chain Fc region.

Antibody Derivatives

The antibodies of the present invention can be further modified tocontain additional nonproteinaceous moieties that are known in the artand readily available. Preferably, the moieties suitable forderivatization of the antibody are water soluble polymers. Non-limitingexamples of water soluble polymers include, but are not limited to,polyethylene glycol (PEG), copolymers of ethylene glycol/propyleneglycol, carboxymethylcellulose, dextran, polyvinyl alcohol, polyvinylpyrrolidone, poly-1,3-dioxolane, poly-1,3,6-trioxane, ethylene/maleicanhydride copolymer, polyaminoacids (either homopolymers or randomcopolymers), and dextran or poly(n-vinyl pyrrolidone)polyethyleneglycol, propropylene glycol homopolymers, prolypropylene oxide/ethyleneoxide co-polymers, polyoxyethylated polyols (e.g., glycerol), polyvinylalcohol, and mixtures thereof. Polyethylene glycol propionaldehyde mayhave advantages in manufacturing due to its stability in water. Thepolymer may be of any molecular weight, and may be branched orunbranched. The number of polymers attached to the antibody may vary,and if more than one polymer are attached, they can be the same ordifferent molecules. In general, the number and/or type of polymers usedfor derivatization can be determined based on considerations including,but not limited to, the particular properties or functions of theantibody to be improved, whether the antibody derivative will be used ina therapy under defined conditions, etc.

In another embodiment, conjugates of an antibody and nonproteinaceousmoiety that may be selectively heated by exposure to radiation areprovided. In one embodiment, the nonproteinaceous moiety is a carbonnanotube (Kam et al., Proc. Natl. Acad. Sci. USA 102: 11600-11605(2005)). The radiation may be of any wavelength, and includes, but isnot limited to, wavelengths that do not harm ordinary cells, but whichheat the nonproteinaceous moiety to a temperature at which cellsproximal to the antibody-nonproteinaceous moiety are killed.

Activity Assays

The antibodies of the present invention can be characterized for theirphysical/chemical properties and biological functions by various assaysknown in the art.

In one aspect, assays are provided for identifying anti-EGFL7 antibodiesthereof having biological activity. Biological activity may include,e.g., the modulation of one or more aspects of EGFL7-associated effects,including but not limited to EGFL7 binding, EGFL7-mediated protection ofendothelial cells under hypoxic stress, and the ability of EGFL7 tomediate endothelial cell adhesion.

In certain embodiments of the invention, the immunoglobulins producedherein are analyzed for their biological activity. In some embodiments,the immunoglobulins of the present invention are tested for theirantigen binding activity. The antigen binding assays that are known inthe art and can be used herein include without limitation any direct orcompetitive binding assays using techniques such as western blots,radioimmunoassays, ELISA (enzyme linked immunosorbent assay), “sandwich”immunoassays, immunoprecipitation assays, fluorescent immunoassays, andprotein A immunoassays. An illustrative antigen binding assay isprovided below in the Examples section.

The purified antibodies can be further characterized by a series ofassays including, but not limited to, N-terminal sequencing, amino acidanalysis, non-denaturing size exclusion high pressure liquidchromatography (HPLC), mass spectrometry, ion exchange chromatographyand papain digestion.

In some embodiments, the present invention contemplates alteredantibodies that possess some but not all effector functions, which makeit a desired candidate for many applications in which the half life ofthe antibody in vivo is important yet certain effector functions (suchas complement and ADCC) are unnecessary or deleterious. In certainembodiments, the Fc activities of the produced immunoglobulin aremeasured to ensure that only the desired properties are maintained. Invitro and/or in vivo cytotoxicity assays can be conducted to confirm thereduction/depletion of CDC and/or ADCC activities. For example, Fcreceptor (FcR) binding assays can be conducted to ensure that theantibody lacks FcγR binding (hence likely lacking ADCC activity), butretains FcRn binding ability. The primary cells for mediating ADCC, NKcells, express FcγRIII only, whereas monocytes express FcγRI, FcγRII andFcγRIII. FcR expression on hematopoietic cells is summarized in Table 3on page 464 of Ravetch and Kinet, Annu. Rev. Immunol 9:457-92 (1991). Anexample of an in vitro assay to assess ADCC activity of a molecule ofinterest is described in U.S. Pat. No. 5,500,362 or 5,821,337. Usefuleffector cells for such assays include peripheral blood mononuclearcells (PBMC) and Natural Killer (NK) cells. Alternatively, oradditionally, ADCC activity of the molecule of interest may be assessedin vivo, e.g., in a animal model such as that disclosed in Clynes et al.PNAS (USA) 95:652-656 (1998). Clq binding assays may also be carried outto confirm that the antibody is unable to bind Clq and hence lacks CDCactivity. To assess complement activation, a CDC assay, e.g. asdescribed in Gazzano-Santoro et al., J. Immunol. Methods 202:163 (1996),may be performed. FcRn binding and in vivo clearance/half lifedeterminations can also be performed using methods known in the art.

In some embodiments, the invention provides altered antibodies thatpossess increased effector functions and/or increased half-life.

Vectors, Host Cells and Recombinant Methods

For recombinant production of an antibody of the invention, the nucleicacid encoding it is isolated and inserted into a replicable vector forfurther cloning (amplification of the DNA) or for expression. DNAencoding the antibody is readily isolated and sequenced usingconventional procedures (e.g., by using oligonucleotide probes that arecapable of binding specifically to genes encoding the heavy and lightchains of the antibody). Many vectors are available. The choice ofvector depends in part on the host cell to be used. Generally, preferredhost cells are of either prokaryotic or eukaryotic (generally mammalian)origin. It will be appreciated that constant regions of any isotype canbe used for this purpose, including IgG, IgM, IgA, IgD, and IgE constantregions, and that such constant regions can be obtained from any humanor animal species.

a. Generating Antibodies Using Prokaryotic Host Cells:

i. Vector Construction

Polynucleotide sequences encoding polypeptide components of the antibodyof the invention can be obtained using standard recombinant techniques.Desired polynucleotide sequences may be isolated and sequenced fromantibody producing cells such as hybridoma cells. Alternatively,polynucleotides can be synthesized using nucleotide synthesizer or PCRtechniques. Once obtained, sequences encoding the polypeptides areinserted into a recombinant vector capable of replicating and expressingheterologous polynucleotides in prokaryotic hosts. Many vectors that areavailable and known in the art can be used for the purpose of thepresent invention. Selection of an appropriate vector will depend mainlyon the size of the nucleic acids to be inserted into the vector and theparticular host cell to be transformed with the vector. Each vectorcontains various components, depending on its function (amplification orexpression of heterologous polynucleotide, or both) and itscompatibility with the particular host cell in which it resides. Thevector components generally include, but are not limited to: an originof replication, a selection marker gene, a promoter, a ribosome bindingsite (RBS), a signal sequence, the heterologous nucleic acid insert anda transcription termination sequence.

In general, plasmid vectors containing replicon and control sequenceswhich are derived from species compatible with the host cell are used inconnection with these hosts. The vector ordinarily carries a replicationsite, as well as marking sequences which are capable of providingphenotypic selection in transformed cells. For example, E. coli istypically transformed using pBR322, a plasmid derived from an E. colispecies. pBR322 contains genes encoding ampicillin (Amp) andtetracycline (Tet) resistance and thus provides easy means foridentifying transformed cells. pBR322, its derivatives, or othermicrobial plasmids or bacteriophage may also contain, or be modified tocontain, promoters which can be used by the microbial organism forexpression of endogenous proteins. Examples of pBR322 derivatives usedfor expression of particular antibodies are described in detail inCarter et al., U.S. Pat. No. 5,648,237.

In addition, phage vectors containing replicon and control sequencesthat are compatible with the host microorganism can be used astransforming vectors in connection with these hosts. For example,bacteriophage such as λGEM™-11 may be utilized in making a recombinantvector which can be used to transform susceptible host cells such as E.coli LE392.

The expression vector of the invention may comprise two or morepromoter-cistron pairs, encoding each of the polypeptide components. Apromoter is an untranslated regulatory sequence located upstream (5′) toa cistron that modulates its expression. Prokaryotic promoters typicallyfall into two classes, inducible and constitutive. Inducible promoter isa promoter that initiates increased levels of transcription of thecistron under its control in response to changes in the culturecondition, e.g. the presence or absence of a nutrient or a change intemperature.

A large number of promoters recognized by a variety of potential hostcells are well known. The selected promoter can be operably linked tocistron DNA encoding the light or heavy chain by removing the promoterfrom the source DNA via restriction enzyme digestion and inserting theisolated promoter sequence into the vector of the invention. Both thenative promoter sequence and many heterologous promoters may be used todirect amplification and/or expression of the target genes. In someembodiments, heterologous promoters are utilized, as they generallypermit greater transcription and higher yields of expressed target geneas compared to the native target polypeptide promoter.

Promoters suitable for use with prokaryotic hosts include the PhoApromoter, the (3-galactamase and lactose promoter systems, a tryptophan(trp) promoter system and hybrid promoters such as the tac or the trcpromoter. However, other promoters that are functional in bacteria (suchas other known bacterial or phage promoters) are suitable as well. Theirnucleotide sequences have been published, thereby enabling a skilledworker operably to ligate them to cistrons encoding the target light andheavy chains (Siebenlist et al. (1980) Cell 20: 269) using linkers oradaptors to supply any required restriction sites.

In one aspect of the invention, each cistron within the recombinantvector comprises a secretion signal sequence component that directstranslocation of the expressed polypeptides across a membrane. Ingeneral, the signal sequence may be a component of the vector, or it maybe a part of the target polypeptide DNA that is inserted into thevector. The signal sequence selected for the purpose of this inventionshould be one that is recognized and processed (i.e. cleaved by a signalpeptidase) by the host cell. For prokaryotic host cells that do notrecognize and process the signal sequences native to the heterologouspolypeptides, the signal sequence is substituted by a prokaryotic signalsequence selected, for example, from the group consisting of thealkaline phosphatase, penicillinase, Ipp, or heat-stable enterotoxin II(STII) leaders, LamB, PhoE, PelB, OmpA and MBP. In one embodiment of theinvention, the signal sequences used in both cistrons of the expressionsystem are STII signal sequences or variants thereof.

In another aspect, the production of the immunoglobulins according tothe invention can occur in the cytoplasm of the host cell, and thereforedoes not require the presence of secretion signal sequences within eachcistron. In that regard, immunoglobulin light and heavy chains areexpressed, folded and assembled to form functional immunoglobulinswithin the cytoplasm. Certain host strains (e.g., the E. colitrxB-strains) provide cytoplasm conditions that are favorable fordisulfide bond formation, thereby permitting proper folding and assemblyof expressed protein subunits. Proba and Pluckthun Gene, 159:203 (1995).

Prokaryotic host cells suitable for expressing antibodies of theinvention include Archaebacteria and Eubacteria, such as Gram-negativeor Gram-positive organisms. Examples of useful bacteria includeEscherichia (e.g., E. coli), Bacilli (e.g., B. subtilis),Enterobacteria, Pseudomonas species (e.g., P. aeruginosa), Salmonellatyphimurium, Serratia marcescans, Klebsiellai, Proteus, Shigella,Rhizobia, Vitreoscilla, or Paracoccus. In one embodiment, gram-negativecells are used. In one embodiment, E. coli cells are used as hosts forthe invention. Examples of E. coli strains include strain W3110(Bachmann, Cellular and Molecular Biology, vol. 2 (Washington, D.C.:American Society for Microbiology, 1987), pp. 1190-1219; ATCC DepositNo. 27,325) and derivatives thereof, including strain 33D3 havinggenotype W3110 ΔfhuΔ (ΔtonΔ) ptr3 lac Iq lacL8 ΔompTΔ(nmpc-fepE) degP41kanR (U.S. Pat. No. 5,639,635). Other strains and derivatives thereof,such as E. coli 294 (ATCC® 31,446), E. coli B, E. coliλ 1776 (ATCC®31,537) and E. coli RV308(ATCC® 31,608) are also suitable. Theseexamples are illustrative rather than limiting. Methods for constructingderivatives of any of the above-mentioned bacteria having definedgenotypes are known in the art and described in, for example, Bass etal., Proteins, 8:309-314 (1990). It is generally necessary to select theappropriate bacteria taking into consideration replicability of thereplicon in the cells of a bacterium. For example, E. coli, Serratia, orSalmonella species can be suitably used as the host when well knownplasmids such as pBR322, pBR325, pACYC177, or pKN410 are used to supplythe replicon. Typically the host cell should secrete minimal amounts ofproteolytic enzymes, and additional protease inhibitors may desirably beincorporated in the cell culture.

ii. Antibody Production

Host cells are transformed with the above-described expression vectorsand cultured in conventional nutrient media modified as appropriate forinducing promoters, selecting transformants, or amplifying the genesencoding the desired sequences.

Transformation means introducing DNA into the prokaryotic host so thatthe DNA is replicable, either as an extrachromosomal element or bychromosomal integrant. Depending on the host cell used, transformationis done using standard techniques appropriate to such cells. The calciumtreatment employing calcium chloride is generally used for bacterialcells that contain substantial cell-wall barriers. Another method fortransformation employs polyethylene glycol/DMSO. Yet another techniqueused is electroporation.

Prokaryotic cells used to produce the polypeptides of the invention aregrown in media known in the art and suitable for culture of the selectedhost cells. Examples of suitable media include luria broth (LB) plusnecessary nutrient supplements. In some embodiments, the media alsocontains a selection agent, chosen based on the construction of theexpression vector, to selectively permit growth of prokaryotic cellscontaining the expression vector. For example, ampicillin is added tomedia for growth of cells expressing ampicillin resistant gene.

Any necessary supplements besides carbon, nitrogen, and inorganicphosphate sources may also be included at appropriate concentrationsintroduced alone or as a mixture with another supplement or medium suchas a complex nitrogen source. Optionally the culture medium may containone or more reducing agents selected from the group consisting ofglutathione, cysteine, cystamine, thioglycollate, dithioerythritol anddithiothreitol.

The prokaryotic host cells are cultured at suitable temperatures. For E.coli growth, for example, the preferred temperature ranges from about20° C. to about 39° C., more preferably from about 25° C. to about 37°C., even more preferably at about 30° C. The pH of the medium may be anypH ranging from about 5 to about 9, depending mainly on the hostorganism. For E. coli, the pH is preferably from about 6.8 to about 7.4,and more preferably about 7.0.

If an inducible promoter is used in the expression vector of theinvention, protein expression is induced under conditions suitable forthe activation of the promoter. In one aspect of the invention, PhoApromoters are used for controlling transcription of the polypeptides.Accordingly, the transformed host cells are cultured in aphosphate-limiting medium for induction. Preferably, thephosphate-limiting medium is the C.R.A.P medium (see, e.g., Simmons etal., J. Immunol. Methods (2002), 263:133-147). A variety of otherinducers may be used, according to the vector construct employed, as isknown in the art.

In one embodiment, the expressed polypeptides of the present inventionare secreted into and recovered from the periplasm of the host cells.Protein recovery typically involves disrupting the microorganism,generally by such means as osmotic shock, sonication or lysis. Oncecells are disrupted, cell debris or whole cells may be removed bycentrifugation or filtration. The proteins may be further purified, forexample, by affinity resin chromatography. Alternatively, proteins canbe transported into the culture media and isolated therein. Cells may beremoved from the culture and the culture supernatant being filtered andconcentrated for further purification of the proteins produced. Theexpressed polypeptides can be further isolated and identified usingcommonly known methods such as polyacrylamide gel electrophoresis (PAGE)and Western blot assay.

In one aspect of the invention, antibody production is conducted inlarge quantity by a fermentation process. Various large-scale fed-batchfermentation procedures are available for production of recombinantproteins. Large-scale fermentations have at least 1000 liters ofcapacity, preferably about 1,000 to 100,000 liters of capacity. Thesefermentors use agitator impellers to distribute oxygen and nutrients,especially glucose (the preferred carbon/energy source). Small scalefermentation refers generally to fermentation in a fermentor that is nomore than approximately 100 liters in volumetric capacity, and can rangefrom about 1 liter to about 100 liters.

In a fermentation process, induction of protein expression is typicallyinitiated after the cells have been grown under suitable conditions to adesired density, e.g., an OD550 of about 180-220, at which stage thecells are in the early stationary phase. A variety of inducers may beused, according to the vector construct employed, as is known in the artand described above. Cells may be grown for shorter periods prior toinduction. Cells are usually induced for about 12-50 hours, althoughlonger or shorter induction time may be used.

To improve the production yield and quality of the polypeptides of theinvention, various fermentation conditions can be modified. For example,to improve the proper assembly and folding of the secreted antibodypolypeptides, additional vectors overexpressing chaperone proteins, suchas Dsb proteins (DsbA, DsbB, DsbC, DsbD and or DsbG) or FkpA (apeptidylprolyl cis,trans-isomerase with chaperone activity) can be usedto co-transform the host prokaryotic cells. The chaperone proteins havebeen demonstrated to facilitate the proper folding and solubility ofheterologous proteins produced in bacterial host cells. Chen et al.(1999) J Bio Chem 274:19601-19605; Georgiou et al., U.S. Pat. No.6,083,715; Georgiou et al., U.S. Pat. No. 6,027,888; Bothmann andPluckthun (2000) J. Biol. Chem. 275:17100-17105; Ramm and Pluckthun(2000) J. Biol. Chem. 275:17106-17113; Arie et al. (2001) Mol.Microbiol. 39:199-210.

To minimize proteolysis of expressed heterologous proteins (especiallythose that are proteolytically sensitive), certain host strainsdeficient for proteolytic enzymes can be used for the present invention.For example, host cell strains may be modified to effect geneticmutation(s) in the genes encoding known bacterial proteases such asProtease III, OmpT, DegP, Tsp, Protease I, Protease Mi, Protease V,Protease VI and combinations thereof. Some E. coli protease-deficientstrains are available and described in, for example, Joly et al. (1998),supra; Georgiou et al., U.S. Pat. No. 5,264,365; Georgiou et al., U.S.Pat. No. 5,508,192; Hara et al., Microbial Drug Resistance, 2:63-72(1996).

In one embodiment, E. coli strains deficient for proteolytic enzymes andtransformed with plasmids overexpressing one or more chaperone proteinsare used as host cells in the expression system of the invention.

iii. Antibody Purification

Standard protein purification methods known in the art can be employed.The following procedures are exemplary of suitable purificationprocedures: fractionation on immunoaffinity or ion-exchange columns,ethanol precipitation, reverse phase HPLC, chromatography on silica oron a cation-exchange resin such as DEAE, chromatofocusing, SDS-PAGE,ammonium sulfate precipitation, and gel filtration using, for example,Sephadex® G-75.

In one aspect, Protein A immobilized on a solid phase is used forimmunoaffinity purification of the full length antibody products of theinvention. Protein A is a 41 kD cell wall protein from Staphylococcusaureas which binds with a high affinity to the Fc region of antibodies.Lindmark et al (1983) J. Immunol. Meth. 62:1-13. The solid phase towhich Protein A is immobilized is preferably a column comprising a glassor silica surface, more preferably a controlled pore glass column or asilicic acid column. In some applications, the column has been coatedwith a reagent, such as glycerol, in an attempt to prevent nonspecificadherence of contaminants.

As the first step of purification, the preparation derived from the cellculture as described above is applied onto the Protein A immobilizedsolid phase to allow specific binding of the antibody of interest toProtein A. The solid phase is then washed to remove contaminantsnon-specifically bound to the solid phase. Finally the antibody ofinterest is recovered from the solid phase by elution.

b. Generating Antibodies Using Eukaryotic Host Cells:

The vector components generally include, but are not limited to, one ormore of the following: a signal sequence, an origin of replication, oneor more marker genes, an enhancer element, a promoter, and atranscription termination sequence.

(i) Signal Sequence Component

A vector for use in a eukaryotic host cell may also contain a signalsequence or other polypeptide having a specific cleavage site at theN-terminus of the mature protein or polypeptide of interest. Theheterologous signal sequence selected preferably is one that isrecognized and processed (i.e., cleaved by a signal peptidase) by thehost cell. In mammalian cell expression, mammalian signal sequences aswell as viral secretory leaders, for example, the herpes simplex gDsignal, are available.

The DNA for such precursor region is ligated in reading frame to DNAencoding the antibody.

(ii) Origin of Replication

Generally, an origin of replication component is not needed formammalian expression vectors. For example, the SV40 origin may typicallybe used only because it contains the early promoter.

(iii) Selection Gene Component

Expression and cloning vectors may contain a selection gene, also termeda selectable marker. Typical selection genes encode proteins that (a)confer resistance to antibiotics or other toxins, e.g., ampicillin,neomycin, methotrexate, or tetracycline, (b) complement auxotrophicdeficiencies, where relevant, or (c) supply critical nutrients notavailable from complex media.

One example of a selection scheme utilizes a drug to arrest growth of ahost cell. Those cells that are successfully transformed with aheterologous gene produce a protein conferring drug resistance and thussurvive the selection regimen. Examples of such dominant selection usethe drugs neomycin, mycophenolic acid and hygromycin.

Another example of suitable selectable markers for mammalian cells arethose that enable the identification of cells competent to take up theantibody nucleic acid, such as DHFR, thymidine kinase, metallothionein-Iand -II, preferably primate metallothionein genes, adenosine deaminase,ornithine decarboxylase, etc.

For example, cells transformed with the DHFR selection gene are firstidentified by culturing all of the transformants in a culture mediumthat contains methotrexate (Mtx), a competitive antagonist of DHFR. Anappropriate host cell when wild-type DHFR is employed is the Chinesehamster ovary (CHO) cell line deficient in DHFR activity (e.g., ATCC®CRL-9096).

Alternatively, host cells (particularly wild-type hosts that containendogenous DHFR) transformed or co-transformed with DNA sequencesencoding an antibody, wild-type DHFR protein, and another selectablemarker such as aminoglycoside 3′-phosphotransferase (APH) can beselected by cell growth in medium containing a selection agent for theselectable marker such as an aminoglycosidic antibiotic, e.g.,kanamycin, neomycin, or G418. See U.S. Pat. No. 4,965,199.

(iv) Promoter Component

Expression and cloning vectors usually contain a promoter that isrecognized by the host organism and is operably linked to the antibodypolypeptide nucleic acid. Promoter sequences are known for eukaryotes.Virtually alleukaryotic genes have an AT-rich region locatedapproximately 25 to 30 bases upstream from the site where transcriptionis initiated.

Another sequence found 70 to 80 bases upstream from the start oftranscription of many genes is a CNCAAT (SEQ ID NO: 232) region where Nmay be any nucleotide. At the 3′ end of most eukaryotic genes is anAATAAA (SEQ ID NO: 233) sequence that may be the signal for addition ofthe poly A tail to the 3′ end of the coding sequence. All of thesesequences are suitably inserted into eukaryotic expression vectors.

Antibody polypeptide transcription from vectors in mammalian host cellsis controlled, for example, by promoters obtained from the genomes ofviruses such as polyoma virus, fowlpox virus, adenovirus (such asAdenovirus 2), bovine papilloma virus, avian sarcoma virus,cytomegalovirus, a retrovirus, hepatitis-B virus and Simian Virus 40(SV40), from heterologous mammalian promoters, e.g., the actin promoteror an immunoglobulin promoter, from heat-shock promoters, provided suchpromoters are compatible with the host cell systems.

The early and late promoters of the SV40 virus are conveniently obtainedas an SV40 restriction fragment that also contains the SV40 viral originof replication. The immediate early promoter of the humancytomegalovirus is conveniently obtained as a HindIII E restrictionfragment. A system for expressing DNA in mammalian hosts using thebovine papilloma virus as a vector is disclosed in U.S. Pat. No.4,419,446. A modification of this system is described in U.S. Pat. No.4,601,978. Alternatively, the Rous Sarcoma Virus long terminal repeatcan be used as the promoter.

(v) Enhancer Element Component

Transcription of DNA encoding the antibody polypeptide of this inventionby higher eukaryotes is often increased by inserting an enhancersequence into the vector. Many enhancer sequences are now known frommammalian genes (globin, elastase, albumin, α-fetoprotein, and insulin).Typically, however, one will use an enhancer from a eukaryotic cellvirus. Examples include the SV40 enhancer on the late side of thereplication origin (bp 100-270), the cytomegalovirus early promoterenhancer, the polyoma enhancer on the late side of the replicationorigin, and adenovirus enhancers. See also Yaniv, Nature 297:17-18(1982) on enhancing elements for activation of eukaryotic promoters. Theenhancer may be spliced into the vector at a position 5′ or 3′ to theantibody polypeptide-encoding sequence, but is preferably located at asite 5′ from the promoter.

(vi) Transcription Termination Component

Expression vectors used in eukaryotic host cells will typically alsocontain sequences necessary for the termination of transcription and forstabilizing the mRNA. Such sequences are commonly available from the 5′and, occasionally 3′, untranslated regions of eukaryotic or viral DNAsor cDNAs. These regions contain nucleotide segments transcribed aspolyadenylated fragments in the untranslated portion of the mRNAencoding an antibody. One useful transcription termination component isthe bovine growth hormone polyadenylation region. See WO94/11026 and theexpression vector disclosed therein.

(vii) Selection and Transformation of Host Cells

Suitable host cells for cloning or expressing the DNA in the vectorsherein include higher eukaryote cells described herein, includingvertebrate host cells. Propagation of vertebrate cells in culture(tissue culture) has become a routine procedure. Examples of usefulmammalian host cell lines are monkey kidney CV1 line transformed by SV40(COS-7, ATCC® CRL 1651); human embryonic kidney line (293 or 293 cellssubcloned for growth in suspension culture, Graham et al., J. Gen Virol.36:59 (1977)); baby hamster kidney cells (BHK, ATCC® CCL 10); Chinesehamster ovary cells/−DHFR(CHO, Urlaub et al., Proc. Natl. Acad. Sci. USA77:4216 (1980)); mouse sertoli cells (TM4, Mather, Biol. Reprod.23:243-251 (1980)); monkey kidney cells (CV1 ATCC® CCL 70); Africangreen monkey kidney cells (VERO-76, ATCC® CRL-1587); human cervicalcarcinoma cells (HELA, ATCC® CCL 2); canine kidney cells (MDCK, ATCC®CCL 34); buffalo rat liver cells (BRL 3A, ATCC® CRL 1442); human lungcells (W138, ATCC® CCL 75); human liver cells (Hep G2, HB 8065); mousemammary tumor (MMT 060562, ATCC® CCL51); TR1 cells (Mather et al.,Annals N.Y. Acad. Sci. 383:44-68 (1982)); MRC 5 cells; FS4 cells; and ahuman hepatoma line (Hep G2).

Host cells are transformed with the above-described expression orcloning vectors for antibody production and cultured in conventionalnutrient media modified as appropriate for inducing promoters, selectingtransformants, or amplifying the genes encoding the desired sequences.

(viii) Culturing the Host Cells

The host cells used to produce an antibody of this invention may becultured in a variety of media. Commercially available media such asHam's F10 (Sigma), Minimal Essential Medium ((MEM), (Sigma), RPMI-1640(Sigma), and Dulbecco's Modified Eagle's Medium ((DMEM), Sigma) aresuitable for culturing the host cells. In addition, any of the mediadescribed in Ham et al., Meth. Enz. 58:44 (1979), Barnes et al., Anal.Biochem. 102:255 (1980), U.S. Pat. No. 4,767,704; 4,657,866; 4,927,762;4,560,655; or 5,122,469; WO 90/03430; WO 87/00195; or U.S. Pat. Re.30,985 may be used as culture media for the host cells. Any of thesemedia may be supplemented as necessary with hormones and/or other growthfactors (such as insulin, transferrin, or epidermal growth factor),salts (such as sodium chloride, calcium, magnesium, and phosphate),buffers (such as HEPES), nucleotides (such as adenosine and thymidine),antibiotics (such as GENTAMYCIN™ drug), trace elements (defined asinorganic compounds usually present at final concentrations in themicromolar range), and glucose or an equivalent energy source. Any othernecessary supplements may also be included at appropriate concentrationsthat would be known to those skilled in the art. The culture conditions,such as temperature, pH, and the like, are those previously used withthe host cell selected for expression, and will be apparent to theordinarily skilled artisan.

(ix) Purification of Antibody

When using recombinant techniques, the antibody can be producedintracellularly, or directly secreted into the medium. If the antibodyis produced intracellularly, as a first step, the particulate debris,either host cells or lysed fragments, are removed, for example, bycentrifugation or ultrafiltration. Where the antibody is secreted intothe medium, supernatants from such expression systems are generallyfirst concentrated using a commercially available protein concentrationfilter, for example, an Amicon or Millipore Pellicon ultrafiltrationunit. A protease inhibitor such as PMSF may be included in any of theforegoing steps to inhibit proteolysis and antibiotics may be includedto prevent the growth of adventitious contaminants.

The antibody composition prepared from the cells can be purified using,for example, hydroxylapatite chromatography, gel electrophoresis,dialysis, and affinity chromatography, with affinity chromatographybeing the preferred purification technique. The suitability of protein Aas an affinity ligand depends on the species and isotype of anyimmunoglobulin Fc domain that is present in the antibody. Protein A canbe used to purify antibodies that are based on human γ1, γ2, or γ4 heavychains (Lindmark et al., J. Immunol. Meth. 62:1-13 (1983)). Protein G isrecommended for all mouse isotypes and for human γ3 (Guss et al., EMBOJ. 5:15671575 (1986)). The matrix to which the affinity ligand isattached is most often agarose, but other matrices are available.Mechanically stable matrices such as controlled pore glass orpoly(styrenedivinyl)benzene allow for faster flow rates and shorterprocessing times than can be achieved with agarose. Where the antibodycomprises a CH3 domain, the Bakerbond ABX™ resin (J. T. Baker,Phillipsburg, N.J.) is useful for purification. Other techniques forprotein purification such as fractionation on an ion-exchange column,ethanol precipitation, Reverse Phase HPLC, chromatography on silica,chromatography on heparin SEPHAROSE™ chromatography on an anion orcation exchange resin (such as a polyaspartic acid column),chromatofocusing, SDS-PAGE, and ammonium sulfate precipitation are alsoavailable depending on the antibody to be recovered.

Following any preliminary purification step(s), the mixture comprisingthe antibody of interest and contaminants may be subjected to low pHhydrophobic interaction chromatography using an elution buffer at a pHbetween about 2.5-4.5, preferably performed at low salt concentrations(e.g., from about 0-0.25M salt).

Immunoconjugates

The invention also provides immunoconjugates (interchangeably referredto as “antibody-drug conjugates,” or “ADCs”) comprising an antibodyconjugated to one or more cytotoxic agents, such as a chemotherapeuticagent, a drug, a growth inhibitory agent, a toxin (e.g., a proteintoxin, an enzymatically active toxin of bacterial, fungal, plant, oranimal origin, or fragments thereof), or a radioactive isotope (i.e., aradioconjugate).

Immunoconjugates have been used for the local delivery of cytotoxicagents, i.e., drugs that kill or inhibit the growth or proliferation ofcells, in the treatment of cancer (Lambert, J. (2005) Curr. Opinion inPharmacology 5:543-549; Wu et al (2005) Nature Biotechnology23(9):1137-1146; Payne, G. (2003) i 3:207-212; Syrigos and Epenetos(1999) Anticancer Research 19:605-614; Niculescu-Duvaz and Springer(1997) Adv. Drug Deliv. Rev. 26:151-172; U.S. Pat. No. 4,975,278).Immunoconjugates allow for the targeted delivery of a drug moiety to atumor, and intracellular accumulation therein, where systemicadministration of unconjugated drugs may result in unacceptable levelsof toxicity to normal cells as well as the tumor cells sought to beeliminated (Baldwin et al., Lancet (Mar. 15, 1986) pp. 603-05; Thorpe(1985) “Antibody Carriers Of Cytotoxic Agents In Cancer Therapy: AReview,” in Monoclonal Antibodies '84: Biological And ClinicalApplications (A. Pinchera et al., eds) pp. 475-506. Both polyclonalantibodies and monoclonal antibodies have been reported as useful inthese strategies (Rowland et al., (1986) Cancer Immunol. Immunother.21:183-87). Drugs used in these methods include daunomycin, doxorubicin,methotrexate, and vindesine (Rowland et al., (1986) supra). Toxins usedin antibody-toxin conjugates include bacterial toxins such as diphtheriatoxin, plant toxins such as ricin, small molecule toxins such asgeldanamycin (Mandler et al (2000) J. Nat. Cancer Inst.92(19):1573-1581; Mandler et al (2000) Bioorganic &Med. Chem. Letters10:1025-1028; Mandler et al (2002) Bioconjugate Chem. 13:786-791),maytansinoids (EP 1391213; Liu et al., (1996) Proc. Natl. Acad. Sci. USA93:8618-8623), and calicheamicin (Lode et al (1998) Cancer Res. 58:2928;Hinman et al (1993) Cancer Res. 53:3336-3342). The toxins may exerttheir cytotoxic effects by mechanisms including tubulin binding, DNAbinding, or topoisomerase inhibition. Some cytotoxic drugs tend to beinactive or less active when conjugated to large antibodies or proteinreceptor ligands.

ZEVALIN® (ibritumomab tiuxetan, Biogen/Idec) is an antibody-radioisotopeconjugate composed of a murine IgG1 kappa monoclonal antibody directedagainst the CD20 antigen found on the surface of normal and malignant Blymphocytes and 111In or 90Y radioisotope bound by a thiourealinker-chelator (Wiseman et al (2000) Eur. Jour. Nucl. Med.27(7):766-77; Wiseman et al (2002) Blood 99(12):4336-42; Witzig et al(2002) J. Clin. Oncol. 20(10):2453-63; Witzig et al (2002) J. Clin.Oncol. 20(15):3262-69). Although ZEVALIN has activity against B-cellnon-Hodgkin's Lymphoma (NHL), administration results in severe andprolonged cytopenias in most patients. MYLOTARG™ (gemtuzumab ozogamicin,Wyeth Pharmaceuticals), an antibody-drug conjugate composed of a huCD33antibody linked to calicheamicin, was approved in 2000 for the treatmentof acute myeloid leukemia by injection (Drugs of the Future (2000)25(7):686; U.S. Pat. Nos. 4,970,198; 5,079,233; 5,585,089; 5,606,040;5,693,762; 5,739,116; 5,767,285; 5,773,001). Cantuzumab mertansine(Immunogen, Inc.), an antibody-drug conjugate composed of the huC242antibody linked via the disulfide linker SPP to the maytansinoid drugmoiety, DM1, is advancing into Phase II trials for the treatment ofcancers that express CanAg, such as colon, pancreatic, gastric, andother cancers. MLN-2704 (Millennium Pharm., BZL Biologics, ImmunogenInc.), an antibody-drug conjugate composed of the anti-prostate specificmembrane antigen (PSMA) monoclonal antibody linked to the maytansinoiddrug moiety, DM1, is under development for the potential treatment ofprostate tumors. The auristatin peptides, auristatin E (AE) andmonomethylauristatin (MMAE), synthetic analogs of dolastatin, wereconjugated to chimeric monoclonal antibodies cBR96 (specific to Lewis Yon carcinomas) and cAC10 (specific to CD30 on hematologicalmalignancies) (Doronina et al (2003) Nature Biotechnol. 21(7):778-784)and are under therapeutic development.

In certain embodiments, an immunoconjugate comprises an antibody and achemotherapeutic agent or other toxin. Chemotherapeutic agents useful inthe generation of immunoconjugates are described herein (e.g., above).Enzymatically active toxins and fragments thereof that can be usedinclude diphtheria A chain, nonbinding active fragments of diphtheriatoxin, exotoxin A chain (from Pseudomonas aeruginosa), ricin A chain,abrin A chain, modeccin A chain, alpha-sarcin, Aleurites fordiiproteins, dianthin proteins, Phytolaca americana proteins (PAPI, PAPII,and PAP-S), momordica charantia inhibitor, curcin, crotin, sapaonariaofficinalis inhibitor, gelonin, mitogellin, restrictocin, phenomycin,enomycin, and the tricothecenes. See, e.g., WO 93/21232 published Oct.28, 1993. A variety of radionuclides are available for the production ofradioconjugated antibodies. Examples include ²¹²Bi, ¹³¹I, ¹³¹In, ⁹⁰Y,and ¹⁸⁶Re. Conjugates of the antibody and cytotoxic agent are made usinga variety of bifunctional protein-coupling agents such asN-succinimidyl-3-(2-pyridyldithiol) propionate (SPDP), iminothiolane(IT), bifunctional derivatives of imidoesters (such as dimethyladipimidate HCl), active esters (such as disuccinimidyl suberate),aldehydes (such as glutaraldehyde), bis-azido compounds (such asbis(p-azidobenzoyl) hexanediamine), bis-diazonium derivatives (such asbis-(p-diazoniumbenzoyl)-ethylenediamine), diisocyanates (such astoluene 2,6-diisocyanate), and bis-active fluorine compounds (such as1,5-difluoro-2,4-dinitrobenzene). For example, a ricin immunotoxin canbe prepared as described in Vitetta et al., Science, 238: 1098 (1987).Carbon-14-labeled 1-isothiocyanatobenzyl-3-methyldiethylenetriaminepentaacetic acid (MX-DTPA) is an exemplary chelating agent forconjugation of radionucleotide to the antibody. See WO94/11026.

Conjugates of an antibody and one or more small molecule toxins, such asa calicheamicin, maytansinoids, dolastatins, aurostatins, atrichothecene, and CC1065, and the derivatives of these toxins that havetoxin activity, are also contemplated herein.

Maytansine and Maytansinoids

In some embodiments, the immunoconjugate comprises an antibody (fulllength or fragments) conjugated to one or more maytansinoid molecules.

Maytansinoids are mitototic inhibitors which act by inhibiting tubulinpolymerization. Maytansine was first isolated from the east Africanshrub Maytenus serrata (U.S. Pat. No. 3,896,111). Subsequently, it wasdiscovered that certain microbes also produce maytansinoids, such asmaytansinol and C-3 maytansinol esters (U.S. Pat. No. 4,151,042).Synthetic maytansinol and derivatives and analogues thereof aredisclosed, for example, in U.S. Pat. Nos. 4,137,230; 4,248,870;4,256,746; 4,260,608; 4,265,814; 4,294,757; 4,307,016; 4,308,268;4,308,269; 4,309,428; 4,313,946; 4,315,929; 4,317,821; 4,322,348;4,331,598; 4,361,650; 4,364,866; 4,424,219; 4,450,254; 4,362,663; and4,371,533.

Maytansinoid drug moieties are attractive drug moieties in antibody drugconjugates because they are: (i) relatively accessible to prepare byfermentation or chemical modification, derivatization of fermentationproducts, (ii) amenable to derivatization with functional groupssuitable for conjugation through the non-disulfide linkers toantibodies, (iii) stable in plasma, and (iv) effective against a varietyof tumor cell lines.

Immunoconjugates containing maytansinoids, methods of making same, andtheir therapeutic use are disclosed, for example, in U.S. Pat. Nos.5,208,020, 5,416,064 and European Patent EP 0 425 235 B1. Liu et al.,Proc. Natl. Acad. Sci. USA 93:8618-8623 (1996) describedimmunoconjugates comprising a maytansinoid designated DM1 linked to themonoclonal antibody C242 directed against human colorectal cancer. Theconjugate was found to be highly cytotoxic towards cultured colon cancercells, and showed antitumor activity in an in vivo tumor growth assay.Chari et al., Cancer Research 52:127-131 (1992) describeimmunoconjugates in which a maytansinoid was conjugated via a disulfidelinker to the murine antibody A7 binding to an antigen on human coloncancer cell lines, or to another murine monoclonal antibody TA. 1 thatbinds the HER-2/neu oncogene. The cytotoxicity of the TA.1-maytansinoidconjugate was tested in vitro on the human breast cancer cell lineSK-BR-3, which expresses 3×10₅ HER-2 surface antigens per cell. The drugconjugate achieved a degree of cytotoxicity similar to the freemaytansinoid drug, which could be increased by increasing the number ofmaytansinoid molecules per antibody molecule. The A7-maytansinoidconjugate showed low systemic cytotoxicity in mice.

Antibody-maytansinoid conjugates are prepared by chemically linking anantibody to a maytansinoid molecule without significantly diminishingthe biological activity of either the antibody or the maytansinoidmolecule. See, e.g., U.S. Pat. No. 5,208,020. An average of 3-4maytansinoid molecules conjugated per antibody molecule has shownefficacy in enhancing cytotoxicity of target cells without negativelyaffecting the function or solubility of the antibody, although even onemolecule of toxin/antibody would be expected to enhance cytotoxicityover the use of naked antibody. Maytansinoids are well known in the artand can be synthesized by known techniques or isolated from naturalsources. Suitable maytansinoids are disclosed, for example, in U.S. Pat.No. 5,208,020 and in the other patents and nonpatent publicationsreferred to hereinabove. Preferred maytansinoids are maytansinol andmaytansinol analogues modified in the aromatic ring or at otherpositions of the maytansinol molecule, such as various maytansinolesters.

There are many linking groups known in the art for makingantibody-maytansinoid conjugates, including, for example, thosedisclosed in U.S. Pat. No. 5,208,020 or EP Patent 0 425 235 B1, Chari etal., Cancer Research 52:127-131 (1992), and U.S. patent application Ser.No. 10/960,602, filed Oct. 8, 2004. Antibody-maytansinoid conjugatescomprising the linker component SMCC may be prepared as disclosed inU.S. patent application Ser. No. 10/960,602, filed Oct. 8, 2004. Thelinking groups include disulfide groups, thioether groups, acid labilegroups, photolabile groups, peptidase labile groups, or esterase labilegroups, as disclosed in the above-identified patents, disulfide andthioether groups being preferred. Additional linking groups aredescribed and exemplified herein.

Conjugates of the antibody and maytansinoid may be made using a varietyof bifunctional protein coupling agents such asN-succinimidyl-3-(2-pyridyldithio)propionate (SPDP),succinimidyl-4-(N-maleimidomethyl)cyclohexane-1-carboxylate (SMCC),iminothiolane (IT), bifunctional derivatives of imidoesters (such asdimethyl adipimidate HCl), active esters (such as disuccinimidylsuberate), aldehydes (such as glutaraldehyde), bis-azido compounds (suchas bis(p-azidobenzoyl)hexanediamine), bis-diazonium derivatives (such asbis-(p-diazoniumbenzoyl)-ethylenediamine), diisocyanates (such astoluene 2,6-diisocyanate), and bis-active fluorine compounds (such as1,5-difluoro-2,4-dinitrobenzene). Particularly preferred coupling agentsinclude N-succinimidyl-3-(2-pyridyldithio)propionate (SPDP) (Carlsson etal., Biochem. J. 173:723-737 (1978)) andN-succinimidyl-4-(2-pyridylthio)pentanoate (SPP) to provide for adisulfide linkage.

The linker may be attached to the maytansinoid molecule at variouspositions, depending on the type of the link. For example, an esterlinkage may be formed by reaction with a hydroxyl group usingconventional coupling techniques. The reaction may occur at the C-3position having a hydroxyl group, the C-14 position modified withhydroxymethyl, the C-15 position modified with a hydroxyl group, and theC-20 position having a hydroxyl group. In a preferred embodiment, thelinkage is formed at the C-3 position of maytansinol or a maytansinolanalogue.

Auristatins and Dolastatins

In some embodiments, the immunoconjugate comprises an antibodyconjugated to dolastatins or dolostatin peptidic analogs andderivatives, the auristatins (U.S. Pat. Nos. 5,635,483; 5,780,588).Dolastatins and auristatins have been shown to interfere withmicrotubule dynamics, GTP hydrolysis, and nuclear and cellular division(Woyke et al (2001) Antimicrob. Agents and Chemother. 45(12):3580-3584)and have anticancer (U.S. Pat. No. 5,663,149) and antifungal activity(Pettit et al (1998) Antimicrob. Agents Chemother. 42:2961-2965). Thedolastatin or auristatin drug moiety may be attached to the antibodythrough the N (amino) terminus or the C (carboxyl) terminus of thepeptidic drug moiety (WO 02/088172).

Exemplary auristatin embodiments include the N-terminus linkedmonomethylauristatin drug moieties DE and DF, disclosed in“Monomethylvaline Compounds Capable of Conjugation to Ligands”, U.S.Ser. No. 10/983,340, filed Nov. 5, 2004.

Typically, peptide-based drug moieties can be prepared by forming apeptide bond between two or more amino acids and/or peptide fragments.Such peptide bonds can be prepared, for example, according to the liquidphase synthesis method (see E. Schroder and K. Lubke, “The Peptides”,volume 1, pp 76-136, 1965, Academic Press) that is well known in thefield of peptide chemistry. The auristatin/dolastatin drug moieties maybe prepared according to the methods of: U.S. Pat. No. 5,635,483; U.S.Pat. No. 5,780,588; Pettit et al (1989) J. Am. Chem. Soc. 111:5463-5465;Pettit et al (1998) Anti-Cancer Drug Design 13:243-277; Pettit, G. R.,et al. Synthesis, 1996, 719-725; and Pettit et al (1996) J. Chem. Soc.Perkin Trans. 1 5:859-863. See also Doronina (2003) Nat Biotechnol21(7):778-784; “Monomethylvaline Compounds Capable of Conjugation toLigands”, U.S. Ser. No. 10/983,340, filed Nov. 5, 2004 (disclosing,e.g., linkers and methods of preparing monomethylvaline compounds suchas MMAE and MMAF conjugated to linkers).

Calicheamicin

In other embodiments, the immunoconjugate comprises an antibodyconjugated to one or more calicheamicin molecules. The calicheamicinfamily of antibiotics are capable of producing double-stranded DNAbreaks at sub-picomolar concentrations. For the preparation ofconjugates of the calicheamicin family, see U.S. Pat. Nos. 5,712,374,5,714,586, 5,739,116, 5,767,285, 5,770,701, 5,770,710, 5,773,001,5,877,296 (all to American Cyanamid Company). Structural analogues ofcalicheamicin which may be used include, but are not limited to, γ1I,α2I, α3I, N-acetyl-γ1I, PSAG and θI1 (Hinman et al., Cancer Research53:3336-3342 (1993), Lode et al., Cancer Research 58:2925-2928 (1998)and the aforementioned U.S. patents to American Cyanamid). Anotheranti-tumor drug that the antibody can be conjugated is QFA which is anantifolate. Both calicheamicin and QFA have intracellular sites ofaction and do not readily cross the plasma membrane. Therefore, cellularuptake of these agents through antibody mediated internalization greatlyenhances their cytotoxic effects.

Other Cytotoxic Agents

Other antitumor agents that can be conjugated to the antibodies includeBCNU, streptozoicin, vincristine and 5-fluorouracil, the family ofagents known collectively LL-E33288 complex described in U.S. Pat. Nos.5,053,394, 5,770,710, as well as esperamicins (U.S. Pat. No. 5,877,296).

Enzymatically active toxins and fragments thereof which can be usedinclude diphtheria A chain, nonbinding active fragments of diphtheriatoxin, exotoxin A chain (from Pseudomonas aeruginosa), ricin A chain,abrin A chain, modeccin A chain, alpha-sarcin, Aleurites fordiiproteins, dianthin proteins, Phytolaca americana proteins (PAPI, PAPII,and PAP-S), momordica charantia inhibitor, curcin, crotin, sapaonariaofficinalis inhibitor, gelonin, mitogellin, restrictocin, phenomycin,enomycin and the tricothecenes. See, for example, WO 93/21232 publishedOct. 28, 1993.

The present invention further contemplates an immunoconjugate formedbetween an antibody and a compound with nucleolytic activity (e.g., aribonuclease or a DNA endonuclease such as a deoxyribonuclease; DNase).

For selective destruction of the tumor, the antibody may comprise ahighly radioactive atom. A variety of radioactive isotopes are availablefor the production of radioconjugated antibodies. Examples includeAt²¹¹, I¹³¹, I¹²⁵, Y⁹⁰, Re¹⁸⁶, Re¹⁸⁸, Sm¹⁵³ Bi²¹², P³², Pb²¹² andradioactive isotopes of Lu. When the conjugate is used for detection, itmay comprise a radioactive atom for scintigraphic studies, for exampletc99m or I123, or a spin label for nuclear magnetic resonance (NMR)imaging (also known as magnetic resonance imaging, mri), such asiodine-123 again, iodine-131, indium-111, fluorine-19, carbon-13,nitrogen-15, oxygen-17, gadolinium, manganese or iron.

The radio- or other labels may be incorporated in the conjugate in knownways. For example, the peptide may be biosynthesized or may besynthesized by chemical amino acid synthesis using suitable amino acidprecursors involving, for example, fluorine-19 in place of hydrogen.Labels such as tc99m or 1123, Re¹⁸⁶, Re¹⁸⁸ and In¹¹¹ can be attached viaa cysteine residue in the peptide. Yttrium-90 can be attached via alysine residue. The IODOGEN method (Fraker et al (1978) Biochem.Biophys. Res. Commun. 80: 49-57) can be used to incorporate iodine-123.“Monoclonal Antibodies in Immunoscintigraphy” (Chatal, CRC Press 1989)describes other methods in detail.

Conjugates of the antibody and cytotoxic agent may be made using avariety of bifunctional protein coupling agents such asN-succinimidyl-3-(2-pyridyldithio)propionate (SPDP),succinimidyl-4-(N-maleimidomethyl)cyclohexane-1-carboxylate (SMCC),iminothiolane (IT), bifunctional derivatives of imidoesters (such asdimethyl adipimidate HCl), active esters (such as disuccinimidylsuberate), aldehydes (such as glutaraldehyde), bis-azido compounds (suchas bis(p-azidobenzoyl)hexanediamine), bis-diazonium derivatives (such asbis-(p-diazoniumbenzoyl)-ethylenediamine), diisocyanates (such astoluene 2,6-diisocyanate), and bis-active fluorine compounds (such as1,5-difluoro-2,4-dinitrobenzene). For example, a ricin immunotoxin canbe prepared as described in Vitetta et al., Science 238:1098 (1987).Carbon-14-labeled 1-isothiocyanatobenzyl-3-methyldiethylenetriaminepentaacetic acid (MX-DTPA) is an exemplary chelating agent forconjugation of radionucleotide to the antibody. See WO94/11026. Thelinker may be a “cleavable linker” facilitating release of the cytotoxicdrug in the cell. For example, an acid-labile linker,peptidase-sensitive linker, photolabile linker, dimethyl linker ordisulfide-containing linker (Chari et al., Cancer Research 52:127-131(1992); U.S. Pat. No. 5,208,020) may be used.

The compounds expressly contemplate, but are not limited to, ADCprepared with cross-linker reagents: BMPS, EMCS, GMBS, HBVS, LC-SMCC,MBS, MPBH, SBAP, SIA, SIAB, SMCC, SMPB, SMPH, sulfo-EMCS, sulfo-GMBS,sulfo-KMUS, sulfo-MBS, sulfo-SIAB, sulfo-SMCC, and sulfo-SMPB, and SVSB(succinimidyl-(4-vinylsulfone)benzoate) which are commercially available(e.g., from Pierce Biotechnology, Inc., Rockford, Ill., U.S.A). Seepages 467-498, 2003-2004 Applications Handbook and Catalog.

Preparation of Antibody Drug Conjugates

In the antibody drug conjugates (ADC), an antibody (Ab) is conjugated toone or more drug moieties (D), e.g. about 1 to about 20 drug moietiesper antibody, through a linker (L). The ADC of Formula I may be preparedby several routes, employing organic chemistry reactions, conditions,and reagents known to those skilled in the art, including: (1) reactionof a nucleophilic group of an antibody with a bivalent linker reagent,to form Ab-L, via a covalent bond, followed by reaction with a drugmoiety D; and (2) reaction of a nucleophilic group of a drug moiety witha bivalent linker reagent, to form D-L, via a covalent bond, followed byreaction with the nucleophilic group of an antibody. Additional methodsfor preparing ADC are described herein.

Ab-(L-D)_(p)  I

The linker may be composed of one or more linker components. Exemplarylinker components include 6-maleimidocaproyl (“MC”), maleimidopropanoyl(“MP”), valine-citrulline (“val-cit”), alanine-phenylalanine(“ala-phe”), p-aminobenzyloxycarbonyl (“PAB”), N-Succinimidyl4-(2-pyridylthio)pentanoate (“SPP”), N-Succinimidyl4-(N-maleimidomethyl)cyclohexane-1 carboxylate (“SMCC’), andN-Succinimidyl (4-iodo-acetyl)aminobenzoate (“SIAB”). Additional linkercomponents are known in the art and some are described herein. See also“Monomethylvaline Compounds Capable of Conjugation to Ligands”, U.S.Ser. No. 10/983,340, filed Nov. 5, 2004.

In some embodiments, the linker may comprise amino acid residues.Exemplary amino acid linker components include a dipeptide, atripeptide, a tetrapeptide or a pentapeptide. Exemplary dipeptidesinclude: valine-citrulline (vc or val-cit), alanine-phenylalanine (af orala-phe). Exemplary tripeptides include: glycine-valine-citrulline(gly-val-cit) and glycine-glycine-glycine (gly-gly-gly). Amino acidresidues which comprise an amino acid linker component include thoseoccurring naturally, as well as minor amino acids and non-naturallyoccurring amino acid analogs, such as citrulline. Amino acid linkercomponents can be designed and optimized in their selectivity forenzymatic cleavage by a particular enzymes, for example, atumor-associated protease, cathepsin B, C and D, or a plasmin protease.

Nucleophilic groups on antibodies include, but are not limited to: (i)N-terminal amine groups, (ii) side chain amine groups, e.g. lysine,(iii) side chain thiol groups, e.g. cysteine, and (iv) sugar hydroxyl oramino groups where the antibody is glycosylated. Amine, thiol, andhydroxyl groups are nucleophilic and capable of reacting to formcovalent bonds with electrophilic groups on linker moieties and linkerreagents including: (i) active esters such as NHS esters, HOBt esters,haloformates, and acid halides; (ii) alkyl and benzyl halides such ashaloacetamides; (iii) aldehydes, ketones, carboxyl, and maleimidegroups. Certain antibodies have reducible interchain disulfides, i.e.cysteine bridges. Antibodies may be made reactive for conjugation withlinker reagents by treatment with a reducing agent such as DTT(dithiothreitol). Each cysteine bridge will thus form, theoretically,two reactive thiol nucleophiles. Additional nucleophilic groups can beintroduced into antibodies through the reaction of lysines with2-iminothiolane (Traut's reagent) resulting in conversion of an amineinto a thiol. Reactive thiol groups may be introduced into the antibody(or fragment thereof) by introducing one, two, three, four, or morecysteine residues (e.g., preparing mutant antibodies comprising one ormore non-native cysteine amino acid residues).

Antibody drug conjugates may also be produced by modification of theantibody to introduce electrophilic moieties, which can react withnucleophilic substituents on the linker reagent or drug. The sugars ofglycosylated antibodies may be oxidized, e.g. with periodate oxidizingreagents, to form aldehyde or ketone groups which may react with theamine group of linker reagents or drug moieties. The resulting imineSchiff base groups may form a stable linkage, or may be reduced, e.g. byborohydride reagents to form stable amine linkages. In one embodiment,reaction of the carbohydrate portion of a glycosylated antibody witheither glactose oxidase or sodium meta-periodate may yield carbonyl(aldehyde and ketone) groups in the protein that can react withappropriate groups on the drug (Hermanson, Bioconjugate Techniques). Inanother embodiment, proteins containing N-terminal serine or threonineresidues can react with sodium meta-periodate, resulting in productionof an aldehyde in place of the first amino acid (Geoghegan & Stroh,(1992) Bioconjugate Chem. 3:138-146; U.S. Pat. No. 5,362,852). Suchaldehyde can be reacted with a drug moiety or linker nucleophile.

Likewise, nucleophilic groups on a drug moiety include, but are notlimited to: amine, thiol, hydroxyl, hydrazide, oxime, hydrazine,thiosemicarbazone, hydrazine carboxylate, and arylhydrazide groupscapable of reacting to form covalent bonds with electrophilic groups onlinker moieties and linker reagents including: (i) active esters such asNHS esters, HOBt esters, haloformates, and acid halides; (ii) alkyl andbenzyl halides such as haloacetamides; (iii) aldehydes, ketones,carboxyl, and maleimide groups.

Alternatively, a fusion protein comprising the antibody and cytotoxicagent may be made, e.g., by recombinant techniques or peptide synthesis.The length of DNA may comprise respective regions encoding the twoportions of the conjugate either adjacent one another or separated by aregion encoding a linker peptide which does not destroy the desiredproperties of the conjugate.

In yet another embodiment, the antibody may be conjugated to a“receptor” (such streptavidin) for utilization in tumor pre-targetingwherein the antibody-receptor conjugate is administered to the patient,followed by removal of unbound conjugate from the circulation using aclearing agent and then administration of a “ligand” (e.g., avidin)which is conjugated to a cytotoxic agent (e.g., a radionucleotide).

Pharmaceutical Formulations

Therapeutic formulations comprising an antibody of the invention areprepared for storage by mixing the antibody having the desired degree ofpurity with optional physiologically acceptable carriers, excipients orstabilizers (Remington: The Science and Practice of Pharmacy 20thedition (2000)), in the form of aqueous solutions, lyophilized or otherdried formulations. Acceptable carriers, excipients, or stabilizers arenontoxic to recipients at the dosages and concentrations employed, andinclude buffers such as phosphate, citrate, histidine and other organicacids; antioxidants including ascorbic acid and methionine;preservatives (such as octadecyldimethylbenzyl ammonium chloride;hexamethonium chloride; benzalkonium chloride, benzethonium chloride;phenol, butyl or benzyl alcohol; alkyl parabens such as methyl or propylparaben; catechol; resorcinol; cyclohexanol; 3-pentanol; and m-cresol);low molecular weight (less than about 10 residues) polypeptides;proteins, such as serum albumin, gelatin, or immunoglobulins;hydrophilic polymers such as polyvinylpyrrolidone; amino acids such asglycine, glutamine, asparagine, histidine, arginine, or lysine;monosaccharides, disaccharides, and other carbohydrates includingglucose, mannose, or dextrins; chelating agents such as EDTA; sugarssuch as sucrose, mannitol, trehalose or sorbitol; salt-formingcounter-ions such as sodium; metal complexes (e.g., Zn-proteincomplexes); and/or non-ionic surfactants such as TWEEN™, PLURONICS™ orpolyethylene glycol (PEG).

The formulation herein may also contain more than one active compound asnecessary for the particular indication being treated, preferably thosewith complementary activities that do not adversely affect each other.Such molecules are suitably present in combination in amounts that areeffective for the purpose intended.

The active ingredients may also be entrapped in microcapsule prepared,for example, by coacervation techniques or by interfacialpolymerization, for example, hydroxymethylcellulose orgelatin-microcapsule and poly-(methylmethacylate) microcapsule,respectively, in colloidal drug delivery systems (for example,liposomes, albumin microspheres, microemulsions, nano-particles andnanocapsules) or in macroemulsions. Such techniques are disclosed inRemington: The Science and Practice of Pharmacy 20th edition (2000).

The formulations to be used for in vivo administration must be sterile.This is readily accomplished by filtration through sterile filtrationmembranes.

Sustained-release preparations may be prepared. Suitable examples ofsustained-release preparations include semipermeable matrices of solidhydrophobic polymers containing the immunoglobulin of the invention,which matrices are in the form of shaped articles, e.g., films, ormicrocapsule. Examples of sustained-release matrices include polyesters,hydrogels (for example, poly(2-hydroxyethyl-methacrylate), orpoly(vinylalcohol)), polylactides (U.S. Pat. No. 3,773,919), copolymersof L-glutamic acid and γ ethyl-L-glutamate, non-degradableethylene-vinyl acetate, degradable lactic acid-glycolic acid copolymerssuch as the LUPRON DEPOT™ (injectable microspheres composed of lacticacid-glycolic acid copolymer and leuprolide acetate), andpoly-D-(−)-3-hydroxybutyric acid. While polymers such as ethylene-vinylacetate and lactic acid-glycolic acid enable release of molecules forover 100 days, certain hydrogels release proteins for shorter timeperiods. When encapsulated immunoglobulins remain in the body for a longtime, they may denature or aggregate as a result of exposure to moistureat 37° C., resulting in a loss of biological activity and possiblechanges in immunogenicity. Rational strategies can be devised forstabilization depending on the mechanism involved. For example, if theaggregation mechanism is discovered to be intermolecular S—S bondformation through thio-disulfide interchange, stabilization may beachieved by modifying sulfhydryl residues, lyophilizing from acidicsolutions, controlling moisture content, using appropriate additives,and developing specific polymer matrix compositions.

Uses

An antibody of the present invention may be used in, for example, invitro, ex vivo and in vivo therapeutic methods.

The invention provides methods and compositions useful for modulatingdisease states associated with expression and/or activity of EGFL7, suchas increased expression and/or activity or undesired expression and/oractivity, said methods comprising administration of an effective dose ofan anti-EGFL7 antibody to an individual in need of such treatment.

In one aspect, the invention provides methods for treating or preventinga tumor, a cancer, and/or a cell proliferative disorder, the methodscomprising administering an effective amount of an anti-EGFL7 antibodyto an individual in need of such treatment.

In one aspect, the invention provides methods for inhibitingangiogenesis, the methods comprising administering an effective amountof an anti-EGFL7 antibody to an individual in need of such treatment.

In one aspect, the invention provides methods for enhancing the efficacyof another anti-angiogenic agent, the methods comprising administeringan effective amount of an anti-EGFL7 antibody to an individual in needof such treatment. In some embodiments, the individual has a tumor, acancer, and/or a cell proliferative disorder. In some embodiments, theother anti-angiogenic agent targets VEGF, e.g. an anti-VEGF antibody.

It is understood that any suitable anti-EGFL7 antibody may be used inmethods of treatment, including monoclonal and/or polyclonal antibodies,a human antibody, a chimeric antibody, an affinity-matured antibody, ahumanized antibody, and/or an antibody fragment. In some embodiments,any anti-EGFL7 antibody described herein is used for treatment.

In any of the methods herein, one may administer to the subject orpatient along with the antibody herein an effective amount of a secondmedicament (where the antibody herein is a first medicament), which isanother active agent that can treat the condition in the subject thatrequires treatment. For instance, an antibody of the invention may beco-administered with another antibody, chemotherapeutic agent(s)(including cocktails of chemotherapeutic agents), anti-angiogenicagent(s), immunosuppressive agents(s), cytokine(s), cytokineantagonist(s), and/or growth-inhibitory agent(s). The type of suchsecond medicament depends on various factors, including the type ofdisorder, the severity of the disease, the condition and age of thepatient, the type and dose of first medicament employed, etc.

Where an antibody of the invention inhibits tumor growth, for example,it may be particularly desirable to combine it with one or more othertherapeutic agents that also inhibit tumor growth. For instance, anantibody of the invention may be combined with an anti-angiogenic agent,such as an anti-VEGF antibody (e.g., AVASTIN®) and/or anti-ErbBantibodies (e.g. HERCEPTIN® trastuzumab anti-HER2 antibody or ananti-HER2 antibody that binds to Domain II of HER2, such as OMNITARG™pertuzumab anti-HER2 antibody) in a treatment scheme, e.g. in treatingany of the disease described herein, including colorectal cancer, lungcancer, hepatocellular carcinoma, breast cancer and/or pancreaticcancer. In some instances, the previous combinations may be accomplishedusing a bispecific antibody. Alternatively, or additionally, the patientmay receive combined radiation therapy (e.g. external beam irradiationor therapy with a radioactive labeled agent, such as an antibody). Suchcombined therapies noted above include combined administration (wherethe two or more agents are included in the same or separateformulations), and separate administration, in which case,administration of the antibody of the invention can occur prior to,and/or following, administration of the adjunct therapy or therapies. Inaddition, combining an antibody of this invention with a relativelynon-cytotoxic agent such as another biologic molecule, e.g., anotherantibody is expected to reduce cytotoxicity versus combining theantibody with a chemotherapeutic agent of other agent that is highlytoxic to cells.

Treatment with a combination of the antibody herein with one or moresecond medicaments preferably results in an improvement in the signs orsymptoms of cancer. For instance, such therapy may result in animprovement in survival (overall survival and/or progression-freesurvival) relative to a patient treated with the second medicament only(e.g., a chemotherapeutic agent only), and/or may result in an objectiveresponse *(partial or complete, preferably complete). Moreover,treatment with the combination of an antibody herein and one or moresecond medicament(s) preferably results in an additive, and morepreferably synergistic (or greater than additive), therapeutic benefitto the patient. Preferably, in this combination method the timingbetween at least one administration of the second medicament and atleast one administration of the antibody herein is about one month orless, more preferably, about two weeks or less.

For treatment of cancers, the second medicament is preferably anotherantibody, chemotherapeutic agent (including cocktails ofchemotherapeutic agents), anti-angiogenic agent, immunosuppressiveagent, prodrug, cytokine, cytokine antagonist, cytotoxic radiotherapy,corticosteroid, anti-emetic, cancer vaccine, analgesic, anti-vascularagent, and/or growth-inhibitory agent. The cytotoxic agent includes anagent interacting with DNA, the antimetabolites, the topoisomerase I orII inhibitors, or the spindle inhibitor or stabilizer agents (e.g.,preferably vinca alkaloid, more preferably selected from vinblastine,deoxyvinblastine, vincristine, vindesine, vinorelbine, vinepidine,vinfosiltine, vinzolidine and vinfunine), or any agent used inchemotherapy such as 5-FU, a taxane, doxorubicin, or dexamethasone.

In some embodiments, the second medicament is another antibody used totreat cancers such as those directed against the extracellular domain ofthe HER2/neu receptor, e.g., trastuzumab, or one of its functionalfragments, pan-HER inhibitor, a Src inhibitor, a MEK inhibitor, or anEGFR inhibitor (e.g., an anti-EGFR antibody (such as one inhibiting thetyrosine kinase activity of the EGFR), which is preferably the mousemonoclonal antibody 225, its mouse-man chimeric derivative C225, or ahumanized antibody derived from this antibody 225 or derived naturalagents, dianilinophthalimides, pyrazolo- or pyrrolopyridopyrimidines,quinazilines, gefitinib, erlotinib, cetuximab, ABX-EFG, canertinib,EKB-569 and PKI-166), or dual-EGFR/HER-2 inhibitor such as lapatanib.

Additional second medicaments include alemtuzumab (CAMPATH™), FavID(IDKLH), CD20 antibodies with altered glycosylation, such asGA-101/GLYCART™, oblimersen (GENASENSE™), thalidomide and analogsthereof, such as lenalidomide (REVLIMID™), imatinib, sorafenib,ofatumumab (HUMAX-CD20™), anti-CD40 antibody, e.g. SGN-40, andanti-CD-80 antibody, e.g. galiximab.

The anti-emetic agent is preferably ondansetron hydrochloride,granisetron hydrochloride, metroclopramide, domperidone, haloperidol,cyclizine, lorazepam, prochlorperazine, dexamethasone, levomepromazine,or tropisetron. The vaccine is preferably GM-CSF DNA and cell-basedvaccines, dendritic cell vaccine, recombinant viral vaccines, heat shockprotein (HSP) vaccines, allogeneic or autologous tumor vaccines. Theanalgesic agent preferably is ibuprofen, naproxen, choline magnesiumtrisalicylate, or oxycodone hydrochloride. The anti-vascular agentpreferably is bevacizumab, or rhuMAb-VEGF. Further second medicamentsinclude anti-proliferative agents such a farnesyl protein transferaseinhibitors, anti-VEGF inhibitors, p53 inhibitors, or PDGFR inhibitors.The second medicament herein includes also biologic-targeted therapysuch as treatment with antibodies as well as small-molecule-targetedtherapy, for example, against certain receptors.

Many anti-angiogenic agents have been identified and are known in theart, including those listed herein, e.g., listed under Definitions, andby, e.g., Carmeliet and Jain, Nature 407:249-257 (2000); Ferrara et al.,Nature Reviews: Drug Discovery, 3:391-400 (2004); and Sato Int. J. Clin.Oncol., 8:200-206 (2003). See also, US Patent Application US20030055006.In one embodiment, an anti-EGFL7 antibody is used in combination with ananti-VEGF neutralizing antibody (or fragment) and/or another VEGFantagonist or a VEGF receptor antagonist including, but not limited to,for example, soluble VEGF receptor (e.g., VEGFR-1, VEGFR-2, VEGFR-3,neuropilins (e.g., NRP1, NRP2)) fragments, aptamers capable of blockingVEGF or VEGFR, neutralizing anti-VEGFR antibodies, low molecule weightinhibitors of VEGFR tyrosine kinases (RTK), antisense strategies forVEGF, ribozymes against VEGF or VEGF receptors, antagonist variants ofVEGF; and any combinations thereof. Alternatively, or additionally, twoor more angiogenesis inhibitors may optionally be co-administered to thepatient in addition to VEGF antagonist and other agent. In certainembodiment, one or more additional therapeutic agents, e.g., anti-canceragents, can be administered in combination with anti-EGFL7 antibody, theVEGF antagonist, and an anti-angiogenesis agent.

Chemotherapeutic agents useful herein are described supra, e.g., in thedefinition of “chemotherapeutic agent”.

Such second medicaments may be administered within 48 hours after theantibodies herein are administered, or within 24 hours, or within 12hours, or within 3-12 hours after said agent, or may be administeredover a pre-selected period of time, which is preferably about 1 to 2days. Further, the dose of such agent may be sub-therapeutic.

The antibodies herein can be administered concurrently, sequentially, oralternating with the second medicament or upon non-responsiveness withother therapy. Thus, the combined administration of a second medicamentincludes co-administration (concurrent administration), using separateformulations or a single pharmaceutical formulation, and consecutiveadministration in either order, wherein preferably there is a timeperiod while both (or all) medicaments simultaneously exert theirbiological activities. All these second medicaments may be used incombination with each other or by themselves with the first medicament,so that the express “second medicament” as used herein does not mean itis the only medicament besides the first medicament, respectively. Thus,the second medicament need not be one medicament, but may constitute orcomprise more than one such drug.

These second medicaments as set forth herein are generally used in thesame dosages and with administration routes as the first medicaments, orabout from 1 to 99% of the dosages of the first medicaments. If suchsecond medicaments are used at all, preferably, they are used in loweramounts than if the first medicament were not present, especially insubsequent dosings beyond the initial dosing with the first medicament,so as to eliminate or reduce side effects caused thereby.

The invention also provides methods and compositions for inhibiting orpreventing relapse tumor growth or relapse cancer cell growth. Relapsetumor growth or relapse cancer cell growth is used to describe acondition in which patients undergoing or treated with one or morecurrently available therapies (e.g., cancer therapies, such aschemotherapy, radiation therapy, surgery, hormonal therapy and/orbiological therapy/immunotherapy, anti-VEGF antibody therapy,particularly a standard therapeutic regimen for the particular cancer)is not clinically adequate to treat the patients or the patients are nolonger receiving any beneficial effect from the therapy such that thesepatients need additional effective therapy. As used herein, the phrasecan also refer to a condition of the “non-responsive/refractory”patient, e.g., which describe patients who respond to therapy yet sufferfrom side effects, develop resistance, do not respond to the therapy, donot respond satisfactorily to the therapy, etc. In various embodiments,a cancer is relapse tumor growth or relapse cancer cell growth where thenumber of cancer cells has not been significantly reduced, or hasincreased, or tumor size has not been significantly reduced, or hasincreased, or fails any further reduction in size or in number of cancercells. The determination of whether the cancer cells are relapse tumorgrowth or relapse cancer cell growth can be made either in vivo or invitro by any method known in the art for assaying the effectiveness oftreatment on cancer cells, using the art-accepted meanings of “relapse”or “refractory” or “non-responsive” in such a context. A tumor resistantto anti-VEGF treatment is an example of a relapse tumor growth.

The invention provides methods of blocking or reducing relapse tumorgrowth or relapse cancer cell growth in a subject by administeringanti-EGFL7 antibody to block or reduce the relapse tumor growth orrelapse cancer cell growth in subject. In certain embodiments, theantagonist can be administered subsequent to the other cancertherapeutic. In certain embodiments, the anti-EGFL7 antibody isadministered simultaneously with cancer therapy. Alternatively, oradditionally, the anti-EGFL7 antibody therapy alternates with anothercancer therapy, which can be performed in any order. The invention alsoencompasses methods for administering one or more inhibitory antibodiesto prevent the onset or recurrence of cancer in patients predisposed tohaving cancer. Generally, the subject was or is concurrently undergoingcancer therapy. In one embodiment, the cancer therapy is treatment withan anti-angiogenesis agent, e.g., a VEGF antagonist. Theanti-angiogenesis agent includes those known in the art and those foundunder the Definitions herein. In one embodiment, the anti-angiogenesisagent is an anti-VEGF neutralizing antibody or fragment (e.g., humanizedA4.6.1, AVASTIN® (Genentech, South San Francisco, Calif.), Y0317, M4,G6, B20, 2C3, etc.). See, e.g., U.S. Pat. Nos. 6,582,959, 6,884,879,6,703,020; WO98/45332; WO 96/30046; WO94/10202; EP 0666868B1; US PatentApplications 20030206899, 20030190317, 20030203409, and 20050112126;Popkov et al., Journal of Immunological Methods 288:149-164 (2004); and,WO2005012359. Additional agents can be administered in combination withVEGF antagonist and an anti-EGFL7 antibody for blocking or reducingrelapse tumor growth or relapse cancer cell growth.

The antibodies of the invention (and adjunct therapeutic agent) is/areadministered by any suitable means, including parenteral, subcutaneous,intraperitoneal, intrapulmonary, and intranasal, and, if desired forlocal treatment, intralesional administration. Parenteral infusionsinclude intramuscular, intravenous, intraarterial, intraperitoneal, orsubcutaneous administration. In addition, the antibodies are suitablyadministered by pulse infusion, particularly with declining doses of theantibody. Dosing can be by any suitable route, e.g. by injections, suchas intravenous or subcutaneous injections, depending in part on whetherthe administration is brief or chronic.

The location of the binding target of an antibody of the invention maybe taken into consideration in preparation and administration of theantibody. When the binding target is an intracellular molecule, certainembodiments of the invention provide for the antibody or antigen-bindingfragment thereof to be introduced into the cell where the binding targetis located. In one embodiment, an antibody of the invention can beexpressed intracellularly as an intrabody. The term “intrabody,” as usedherein, refers to an antibody or antigen-binding portion thereof that isexpressed intracellularly and that is capable of selectively binding toa target molecule, as described, e.g., in Marasco, Gene Therapy 4: 11-15(1997); Kontermann, Methods 34: 163-170 (2004); U.S. Pat. Nos. 6,004,940and 6,329,173; U.S. Patent Application Publication No. 2003/0104402, andPCT Publication No. WO2003/077945. See also, for example, WO96/07321published Mar. 14, 1996, concerning the use of gene therapy to generateintracellular antibodies.

Intracellular expression of an intrabody may be effected by introducinga nucleic acid encoding the desired antibody or antigen-binding portionthereof (lacking the wild-type leader sequence and secretory signalsnormally associated with the gene encoding that antibody orantigen-binding fragment) into a target cell. One or more nucleic acidsencoding all or a portion of an antibody of the invention can bedelivered to a target cell, such that one or more intrabodies areexpressed which are capable of binding to an intracellular targetpolypeptide and modulating the activity of the target polypeptide. Anystandard method of introducing nucleic acids into a cell may be used,including, but not limited to, microinjection, ballistic injection,electroporation, calcium phosphate precipitation, liposomes, andtransfection with retroviral, adenoviral, adeno-associated viral andvaccinia vectors carrying the nucleic acid of interest.

In certain embodiments, nucleic acid (optionally contained in a vector)may be introduced into a patient's cells by in vivo and ex vivo methods.In one example of in vivo delivery, nucleic acid is injected directlyinto the patient, e.g., at the site where therapeutic intervention isrequired. In a further example of in vivo delivery, nucleic acid isintroduced into a cell using transfection with viral vectors (such asadenovirus, Herpes simplex I virus, or adeno-associated virus) andlipid-based systems (useful lipids for lipid-mediated transfer of thegene are DOTMA, DOPE and DC-Chol, for example). For review of certaingene marking and gene therapy protocols, see Anderson et al., Science256:808-813 (1992), and WO 93/25673 and the references cited therein. Inan example of ex vivo treatment, a patient's cells are removed, nucleicacid is introduced into those isolated cells, and the modified cells areadministered to the patient either directly or, for example,encapsulated within porous membranes which are implanted into thepatient (see, e.g., U.S. Pat. Nos. 4,892,538 and 5,283,187). A commonlyused vector for ex vivo delivery of a nucleic acid is a retroviralvector.

In another embodiment, internalizing antibodies are provided. Antibodiescan possess certain characteristics that enhance delivery of antibodiesinto cells, or can be modified to possess such characteristics.Techniques for achieving this are known in the art. For example,cationization of an antibody is known to facilitate its uptake intocells (see, e.g., U.S. Pat. No. 6,703,019). Lipofections or liposomescan also be used to deliver the antibody into cells. Where antibodyfragments are used, the smallest inhibitory fragment that specificallybinds to the target protein may be advantageous. For example, based uponthe variable-region sequences of an antibody, peptide molecules can bedesigned that retain the ability to bind the target protein sequence.Such peptides can be synthesized chemically and/or produced byrecombinant DNA technology. See, e.g., Marasco et al., Proc. Natl. Acad.Sci. USA, 90: 7889-7893 (1993).

Entry of antibodies into target cells can be enhanced by other methodsknown in the art. For example, certain sequences, such as those derivedfrom HIV Tat or the Antennapedia homeodomain protein are able to directefficient uptake of heterologous proteins across cell membranes. See,e.g., Chen et al., Proc. Natl. Acad. Sci. USA (1999), 96:4325-4329.

When the binding target of an antibody is located in the brain, certainembodiments of the invention provide for the antibody to traverse theblood-brain barrier. Several art-known approaches exist for transportingmolecules across the blood-brain barrier, including, but not limited to,physical methods, lipid-based methods, stem cell-based methods, andreceptor and channel-based methods.

Physical methods of transporting an antibody across the blood-brainbarrier include, but are not limited to, circumventing the blood-brainbarrier entirely, or by creating openings in the blood-brain barrier.Circumvention methods include, but are not limited to, direct injectioninto the brain (see, e.g., Papanastassiou et al., Gene Therapy 9:398-406 (2002)), interstitial infusion/convection-enhanced delivery(see, e.g., Bobo et al., Proc. Natl. Acad. Sci. USA 91: 2076-2080(1994)), and implanting a delivery device in the brain (see, e.g., Gillet al., Nature Med. 9: 589-595 (2003); and Gliadel Wafers™, GuildfordPharmaceutical). Methods of creating openings in the barrier include,but are not limited to, ultrasound (see, e.g., U.S. Patent PublicationNo. 2002/0038086), osmotic pressure (e.g., by administration ofhypertonic mannitol (Neuwelt, E. A., Implication of the Blood-BrainBarrier and its Manipulation, Vols 1 & 2, Plenum Press, N.Y. (1989)),permeabilization by, e.g., bradykinin or permeabilizer A-7 (see, e.g.,U.S. Pat. Nos. 5,112,596, 5,268,164, 5,506,206, and 5,686,416), andtransfection of neurons that straddle the blood-brain barrier withvectors containing genes encoding the antibody (see, e.g., U.S. PatentPublication No. 2003/0083299).

Lipid-based methods of transporting an antibody across the blood-brainbarrier include, but are not limited to, encapsulating the antibody inliposomes that are coupled to antibody binding fragments that bind toreceptors on the vascular endothelium of the blood-brain barrier (see,e.g., U.S. Patent Application Publication No. 20020025313), and coatingthe antibody in low-density lipoprotein particles (see, e.g., U.S.Patent Application Publication No. 20040204354) or apolipoprotein E(see, e.g., U.S. Patent Application Publication No. 20040131692).

Stem-cell based methods of transporting an antibody across theblood-brain barrier entail genetically engineering neural progenitorcells (NPCs) to express the antibody of interest and then implanting thestem cells into the brain of the individual to be treated. See Behrstocket al. (2005) Gene Ther. 15 Dec. 2005 advanced online publication(reporting that NPCs genetically engineered to express the neurotrophicfactor GDNF reduced symptoms of Parkinson disease when implanted intothe brains of rodent and primate models).

Receptor and channel-based methods of transporting an antibody acrossthe blood-brain barrier include, but are not limited to, usingglucocorticoid blockers to increase permeability of the blood-brainbarrier (see, e.g., U.S. Patent Application Publication Nos.2002/0065259, 2003/0162695, and 2005/0124533); activating potassiumchannels (see, e.g., U.S. Patent Application Publication No.2005/0089473), inhibiting ABC drug transporters (see, e.g., U.S. PatentApplication Publication No. 2003/0073713); coating antibodies with atransferrin and modulating activity of the one or more transferrinreceptors (see, e.g., U.S. Patent Application Publication No.2003/0129186), and cationizing the antibodies (see, e.g., U.S. Pat. No.5,004,697).

Antibodies of the invention would be formulated, dosed, and administeredin a fashion consistent with good medical practice. Factors forconsideration in this context include the particular disorder beingtreated, the particular mammal being treated, the clinical condition ofthe individual patient, the cause of the disorder, the site of deliveryof the agent, the method of administration, the scheduling ofadministration, and other factors known to medical practitioners. Theantibody need not be, but is optionally formulated with one or moreagents currently used to prevent or treat the disorder in question. Theeffective amount of such other agents depends on the amount of antibodypresent in the formulation, the type of disorder or treatment, and otherfactors discussed above. These are generally used in the same dosagesand with administration routes as described herein, or about from 1 to99% of the dosages described herein, or in any dosage and by any routethat is empirically/clinically determined to be appropriate.

For the prevention or treatment of disease, the appropriate dosage of anantibody of the invention (when used alone or in combination with one ormore other additional therapeutic agents) will depend on the type ofdisease to be treated, the type of antibody, the severity and course ofthe disease, whether the antibody is administered for preventive ortherapeutic purposes, previous therapy, the patient's clinical historyand response to the antibody, and the discretion of the attendingphysician. The antibody is suitably administered to the patient at onetime or over a series of treatments. Depending on the type and severityof the disease, about 1 μg/kg to 15 mg/kg (e.g. 0.1 mg/kg-10 mg/kg) ofantibody can be an initial candidate dosage for administration to thepatient, whether, for example, by one or more separate administrations,or by continuous infusion. One typical daily dosage might range fromabout 1 μg/kg to 100 mg/kg or more, depending on the factors mentionedabove. For repeated administrations over several days or longer,depending on the condition, the treatment would generally be sustaineduntil a desired suppression of disease symptoms occurs. One exemplarydosage of the antibody would be in the range from about 0.05 mg/kg toabout 10 mg/kg. Thus, one or more doses of about 0.5 mg/kg, 2.0 mg/kg,4.0 mg/kg or 10 mg/kg (or any combination thereof) may be administeredto the patient. Such doses may be administered intermittently, e.g.every week or every three weeks (e.g. such that the patient receivesfrom about two to about twenty, or e.g. about six doses of theantibody). An initial higher loading dose, followed by one or more lowerdoses may be administered. An exemplary dosing regimen comprisesadministering an initial loading dose of about 4 mg/kg, followed by aweekly maintenance dose of about 2 mg/kg of the antibody. However, otherdosage regimens may be useful. The progress of this therapy is easilymonitored by conventional techniques and assays.

Diagnostic Methods and Methods of Detection

The anti-EGFL7 antibodies of the invention are useful in assaysdetecting EGFL7 expression (such as diagnostic or prognostic assays) inspecific cells or tissues wherein the antibodies are labeled asdescribed below and/or are immobilized on an insoluble matrix.

In another aspect, the invention provides methods for detection ofEGFL7, the methods comprising detecting EGFL7-anti-EGFL7 antibodycomplex in the sample. The term “detection” as used herein includesqualitative and/or quantitative detection (measuring levels) with orwithout reference to a control.

In another aspect, the invention provides any of the anti-EGFL7antibodies described herein, wherein the anti-EGFL7 antibody comprises adetectable label.

In another aspect, the invention provides a complex of any of theanti-EGFL7 antibodies described herein and EGFL7. In some embodiments,the complex is in vivo or in vitro. In some embodiments, the complexcomprises a cancer cell. In some embodiments, the anti-EGFL7 antibody isdetectably labeled.

Anti-EGFL7 antibodies (e.g., any of the EGFL7 antibodies describedherein) can be used for the detection of EGFL7 in any one of a number ofwell known detection assay methods.

For example, a biological sample may be assayed for EGFL7 by obtainingthe sample from a desired source, admixing the sample with anti-EGFL7antibody to allow the antibody to form antibody/EGFL7 complex with anyEGFL7 present in the mixture, and detecting any antibody/EGFL7 complexpresent in the mixture. The biological sample may be prepared for assayby methods known in the art which are suitable for the particularsample. The methods of admixing the sample with antibodies and themethods of detecting antibody/EGFL7 complex are chosen according to thetype of assay used. Such assays include immunohistochemistry,competitive and sandwich assays, and steric inhibition assays. Forsample preparation, a tissue or cell sample from a mammal (typically ahuman patient) may be used. Examples of samples include, but are notlimited to, cancer cells such as colon, breast, prostate, ovary, lung,stomach, pancreas, lymphoma, and leukemia cancer cells. EGFL7 may alsobe measured in serum. The sample can be obtained by a variety ofprocedures known in the art including, but not limited to surgicalexcision, aspiration or biopsy. The tissue may be fresh or frozen. Inone embodiment, the sample is fixed and embedded in paraffin or thelike. The tissue sample may be fixed (i.e. preserved) by conventionalmethodology (See e.g., “Manual of Histological Staining Method of theArmed Forces Institute of Pathology,” 3^(rd) edition (1960) Lee G. Luna,HT (ASCP) Editor, The Blakston Division McGraw-Hill Book Company, NewYork; The Armed Forces Institute of Pathology Advanced LaboratoryMethods in Histology and Pathology (1994) Ulreka V. Mikel, Editor, ArmedForces Institute of Pathology, American Registry of Pathology,Washington, D.C.). One of ordinary skill in the art will appreciate thatthe choice of a fixative is determined by the purpose for which thesample is to be histologically stained or otherwise analyzed. One ofordinary skill in the art will also appreciate that the length offixation depends upon the size of the tissue sample and the fixativeused. By way of example, neutral buffered formalin, Bouin's orparaformaldehyde, may be used to fix a sample. Generally, the sample isfirst fixed and is then dehydrated through an ascending series ofalcohols, infiltrated and embedded with paraffin or other sectioningmedia so that the tissue sample may be sectioned. Alternatively, one maysection the tissue and fix the sections obtained. By way of example, thetissue sample may be embedded and processed in paraffin by conventionalmethodology (See e.g., “Manual of Histological Staining Method of theArmed Forces Institute of Pathology”, supra). Examples of paraffin thatmay be used include, but are not limited to, Paraplast, Broloid, andTissuemay. Once the tissue sample is embedded, the sample may besectioned by a microtome or the like (See e.g., “Manual of HistologicalStaining Method of the Armed Forces Institute of Pathology”, supra). Byway of example for this procedure, sections may range from about threemicrons to about five microns in thickness. Once sectioned, the sectionsmay be attached to slides by several standard methods. Examples of slideadhesives include, but are not limited to, silane, gelatin,poly-L-lysine and the like. By way of example, the paraffin embeddedsections may be attached to positively charged slides and/or slidescoated with poly-L-lysine. If paraffin has been used as the embeddingmaterial, the tissue sections are generally deparaffinized andrehydrated to water. The tissue sections may be deparaffinized byseveral conventional standard methodologies. For example, xylenes and agradually descending series of alcohols may be used (See e.g., “Manualof Histological Staining Method of the Armed Forces Institute ofPathology”, supra). Alternatively, commercially availabledeparaffinizing non-organic agents such as Hemo-De7 (CMS, Houston, Tex.)may be used.

Analytical methods for EGFL7 all use one or more of the followingreagents: labeled EGFL7 analogue, immobilized EGFL7 analogue, labeledanti-EGFL7 antibody, immobilized anti-EGFL7 antibody and stericconjugates. The labeled reagents also are known as “tracers.”

The label used is any detectable functionality that does not interferewith the binding of EGFL7 and anti-EGFL7 antibody. Numerous labels areknown for use in immunoassay, examples including moieties that may bedetected directly, such as fluorochrome, chemiluminescent, andradioactive labels, as well as moieties, such as enzymes, that must bereacted or derivatized to be detected.

The label used is any detectable functionality that does not interferewith the binding of EGFL7 and anti-EGFL7 antibody. Numerous labels areknown for use in immunoassay, examples including moieties that may bedetected directly, such as fluorochrome, chemiluminescent, andradioactive labels, as well as moieties, such as enzymes, that must bereacted or derivatized to be detected. Examples of such labels includethe radioisotopes ³²P, ¹⁴C, ¹²⁵I, ³H, and ¹³¹I, fluorophores such asrare earth chelates or fluorescein and its derivatives, rhodamine andits derivatives, dansyl, umbelliferone, luceriferases, e.g., fireflyluciferase and bacterial luciferase (U.S. Pat. No. 4,737,456),luciferin, 2,3-dihydrophthalazinediones, horseradish peroxidase (HRP),alkaline phosphatase, (3-galactosidase, glucoamylase, lysozyme,saccharide oxidases, e.g., glucose oxidase, galactose oxidase, andglucose-6-phosphate dehydrogenase, heterocyclic oxidases such as uricaseand xanthine oxidase, coupled with an enzyme that employs hydrogenperoxide to oxidize a dye precursor such as HRP, lactoperoxidase, ormicroperoxidase, biotin/avidin, spin labels, bacteriophage labels,stable free radicals, and the like.

Conventional methods are available to bind these labels covalently toproteins or polypeptides. For instance, coupling agents such asdialdehydes, carbodiimides, dimaleimides, bis-imidates, bis-diazotizedbenzidine, and the like may be used to tag the antibodies with theabove-described fluorescent, chemiluminescent, and enzyme labels. See,for example, U.S. Pat. Nos. 3,940,475 (fluorimetry) and 3,645,090(enzymes); Hunter et al., Nature, 144: 945 (1962); David et al.,Biochemistry, 13: 1014-1021 (1974); Pain et al., J. Immunol. Methods,40: 219-230 (1981); and Nygren, J. Histochem. and Cytochem., 30: 407-412(1982). Preferred labels herein are enzymes such as horseradishperoxidase and alkaline phosphatase. The conjugation of such label,including the enzymes, to the antibody is a standard manipulativeprocedure for one of ordinary skill in immunoassay techniques. See, forexample, O'Sullivan et al., “Methods for the Preparation ofEnzyme-antibody Conjugates for Use in Enzyme Immunoassay,” in Methods inEnzymology, ed. J. J. Langone and H. Van Vunakis, Vol. 73 (AcademicPress, New York, N.Y., 1981), pp. 147-166.

Immobilization of reagents is required for certain assay methods.Immobilization entails separating the anti-EGFL7 antibody from any EGFL7that remains free in solution. This conventionally is accomplished byeither insolubilizing the anti-EGFL7 antibody or EGFL7 analogue beforethe assay procedure, as by adsorption to a water-insoluble matrix orsurface (Bennich et al., U.S. Pat. No. 3,720,760), by covalent coupling(for example, using glutaraldehyde cross-linking), or by insolubilizingthe anti-EGFL7 antibody or EGFL7 analogue afterward, e.g., byimmunoprecipitation.

The expression of proteins in a sample may be examined usingimmunohistochemistry and staining protocols. Immunohistochemicalstaining of tissue sections has been shown to be a reliable method ofassessing or detecting presence of proteins in a sample.Immunohistochemistry (“IHC”) techniques utilize an antibody to probe andvisualize cellular antigens in situ, generally by chromogenic orfluorescent methods. For sample preparation, a tissue or cell samplefrom a mammal (typically a human patient) may be used. The sample can beobtained by a variety of procedures known in the art including, but notlimited to surgical excision, aspiration or biopsy. The tissue may befresh or frozen. In one embodiment, the sample is fixed and embedded inparaffin or the like. The tissue sample may be fixed (i.e. preserved) byconventional methodology. One of ordinary skill in the art willappreciate that the choice of a fixative is determined by the purposefor which the sample is to be histologically stained or otherwiseanalyzed. One of ordinary skill in the art will also appreciate that thelength of fixation depends upon the size of the tissue sample and thefixative used.

IHC may be performed in combination with additional techniques such asmorphological staining and/or fluorescence in-situ hybridization. Twogeneral methods of IHC are available; direct and indirect assays.According to the first assay, binding of antibody to the target antigen(e.g., EGFL7) is determined directly. This direct assay uses a labeledreagent, such as a fluorescent tag or an enzyme-labeled primaryantibody, which can be visualized without further antibody interaction.In a typical indirect assay, unconjugated primary antibody binds to theantigen and then a labeled secondary antibody binds to the primaryantibody. Where the secondary antibody is conjugated to an enzymaticlabel, a chromogenic or fluorogenic substrate is added to providevisualization of the antigen. Signal amplification occurs becauseseveral secondary antibodies may react with different epitopes on theprimary antibody.

The primary and/or secondary antibody used for immunohistochemistrytypically will be labeled with a detectable moiety. Numerous labels areavailable.

Aside from the sample preparation procedures discussed above, furthertreatment of the tissue section prior to, during or following IHC may bedesired, For example, epitope retrieval methods, such as heating thetissue sample in citrate buffer may be carried out (see, e.g., Leong etal. Appl. Immunohistochem. 4(3):201 (1996)).

Following an optional blocking step, the tissue section is exposed toprimary antibody for a sufficient period of time and under suitableconditions such that the primary antibody binds to the target proteinantigen in the tissue sample. Appropriate conditions for achieving thiscan be determined by routine experimentation. The extent of binding ofantibody to the sample is determined by using any one of the detectablelabels discussed above. Preferably, the label is an enzymatic label(e.g. HRPO) which catalyzes a chemical alteration of the chromogenicsubstrate such as 3,3′-diaminobenzidine chromogen. Preferably theenzymatic label is conjugated to antibody which binds specifically tothe primary antibody (e.g. the primary antibody is rabbit polyclonalantibody and secondary antibody is goat anti-rabbit antibody).

Specimens thus prepared may be mounted and coverslipped. Slideevaluation is then determined, e.g. using a microscope, and stainingintensity criteria, routinely used in the art, may be employed.

Other assay methods, known as competitive or sandwich assays, are wellestablished and widely used in the commercial diagnostics industry.

Competitive assays rely on the ability of a tracer EGFL7 analogue tocompete with the test sample EGFL7 for a limited number of anti-EGFL7antibody antigen-binding sites. The anti-EGFL7 antibody generally isinsolubilized before or after the competition and then the tracer andEGFL7 bound to the anti-EGFL7 antibody are separated from the unboundtracer and EGFL7. This separation is accomplished by decanting (wherethe binding partner was preinsolubilized) or by centrifuging (where thebinding partner was precipitated after the competitive reaction). Theamount of test sample EGFL7 is inversely proportional to the amount ofbound tracer as measured by the amount of marker substance.Dose-response curves with known amounts of EGFL7 are prepared andcompared with the test results to quantitatively determine the amount ofEGFL7 present in the test sample. These assays are called ELISA systemswhen enzymes are used as the detectable markers.

Another species of competitive assay, called a “homogeneous” assay, doesnot require a phase separation. Here, a conjugate of an enzyme with theEGFL7 is prepared and used such that when anti-EGFL7 antibody binds tothe EGFL7 the presence of the anti-EGFL7 antibody modifies the enzymeactivity. In this case, the EGFL7 or its immunologically activefragments are conjugated with a bifunctional organic bridge to an enzymesuch as peroxidase. Conjugates are selected for use with anti-EGFL7antibody so that binding of the anti-EGFL7 antibody inhibits orpotentiates the enzyme activity of the label. This method per se iswidely practiced under the name of EMIT.

Steric conjugates are used in steric hindrance methods for homogeneousassay. These conjugates are synthesized by covalently linking alow-molecular-weight hapten to a small EGFL7 fragment so that antibodyto hapten is substantially unable to bind the conjugate at the same timeas anti-EGFL7 antibody. Under this assay procedure the EGFL7 present inthe test sample will bind anti-EGFL7 antibody, thereby allowinganti-hapten to bind the conjugate, resulting in a change in thecharacter of the conjugate hapten, e.g., a change in fluorescence whenthe hapten is a fluorophore.

Sandwich assays particularly are useful for the determination of EGFL7or anti-EGFL7 antibodies. In sequential sandwich assays an immobilizedanti-EGFL7 antibody is used to adsorb test sample EGFL7, the test sampleis removed as by washing, the bound EGFL7 is used to adsorb a second,labeled anti-EGFL7 antibody and bound material is then separated fromresidual tracer. The amount of bound tracer is directly proportional totest sample EGFL7. In “simultaneous” sandwich assays the test sample isnot separated before adding the labeled anti-EGFL7. A sequentialsandwich assay using an anti-EGFL7 monoclonal antibody as one antibodyand a polyclonal anti-EGFL7 antibody as the other is useful in testingsamples for EGFL7.

The foregoing are merely exemplary detection assays for EGFL7. Othermethods now or hereafter developed that use anti-EGFL7 antibody for thedetermination of EGFL7 are included within the scope hereof, includingthe bioassays described herein.

In one aspect, the invention provides methods to detect (e.g., presenceor absence of or amount) a polynucleotide(s) (e.g., EGFL7polynucleotides) in a biological sample from an individual, such as ahuman subject. A variety of methods for detecting polynucleotides can beemployed and include, for example, RT-PCR, taqman, amplificationmethods, polynucleotide microarray, and the like.

Methods for the detection of polynucleotides (such as mRNA) are wellknown and include, for example, hybridization assays using complementaryDNA probes (such as in situ hybridization using labeled EGFL7riboprobes), Northern blot and related techniques, and various nucleicacid amplification assays (such as RT-PCR using complementary primersspecific for EGFL7, and other amplification type detection methods, suchas, for example, branched DNA, SPIA, Ribo-SPIA, SISBA, TMA and thelike).

Biological samples from mammals can be conveniently assayed for, e.g.,EGFL7 mRNAs using Northern, dot blot or PCR analysis. For example,RT-PCR assays such as quantitative PCR assays are well known in the art.In an illustrative embodiment of the invention, a method for detectingEGFL7 mRNA in a biological sample comprises producing cDNA from thesample by reverse transcription using at least one primer; amplifyingthe cDNA so produced using an EGFL7 polynucleotide as sense andantisense primers to amplify EGFL7 cDNAs therein; and detecting thepresence or absence of the amplified EGFL7 cDNA. In addition, suchmethods can include one or more steps that allow one to determine theamount (levels) of EGFL7 mRNA in a biological sample (e.g. bysimultaneously examining the levels a comparative control mRNA sequenceof a housekeeping gene such as an actin family member). Optionally, thesequence of the amplified EGFL7 cDNA can be determined.

Probes and/or primers may be labeled with a detectable marker, such as,for example, a radioisotope, fluorescent compound, bioluminescentcompound, a chemiluminescent compound, metal chelator or enzyme. Suchprobes and primers can be used to detect the presence of EGFL7polynucleotides in a sample and as a means for detecting a cellexpressing EGFL7 proteins. As will be understood by the skilled artisan,a great many different primers and probes may be prepared (e.g., basedon the sequences provided in herein) and used effectively to amplify,clone and/or determine the presence or absence of and/or amount of EGFL7mRNAs.

Optional methods of the invention include protocols comprising detectionof polynucleotides, such as EGFL7 polynucleotide, in a tissue or cellsample using microarray technologies. For example, using nucleic acidmicroarrays, test and control mRNA samples from test and control tissuesamples are reverse transcribed and labeled to generate cDNA probes. Theprobes are then hybridized to an array of nucleic acids immobilized on asolid support. The array is configured such that the sequence andposition of each member of the array is known. For example, a selectionof genes that have potential to be expressed in certain disease statesmay be arrayed on a solid support. Hybridization of a labeled probe witha particular array member indicates that the sample from which the probewas derived expresses that gene. Differential gene expression analysisof disease tissue can provide valuable information. Microarraytechnology utilizes nucleic acid hybridization techniques and computingtechnology to evaluate the mRNA expression profile of thousands of geneswithin a single experiment. (see, e.g., WO 01/75166 published Oct. 11,2001; (See, for example, U.S. Pat. No. 5,700,637, U.S. Pat. No.5,445,934, and U.S. Pat. No. 5,807,522, Lockart, Nature Biotechnology,14:1675-1680 (1996); Cheung, V. G. et al., Nature Genetics21(Suppl):15-19 (1999) for a discussion of array fabrication). DNAmicroarrays are miniature arrays containing gene fragments that areeither synthesized directly onto or spotted onto glass or othersubstrates. Thousands of genes are usually represented in a singlearray. A typical microarray experiment involves the following steps: 1.preparation of fluorescently labeled target from RNA isolated from thesample, 2. hybridization of the labeled target to the microarray, 3.washing, staining, and scanning of the array, 4. analysis of the scannedimage and 5. generation of gene expression profiles. Currently two maintypes of DNA microarrays are being used: oligonucleotide (usually 25 to70 mers) arrays and gene expression arrays containing PCR productsprepared from cDNAs. In forming an array, oligonucleotides can be eitherprefabricated and spotted to the surface or directly synthesized on tothe surface (in situ).

The Affymetrix GeneChip® system is a commercially available microarraysystem which comprises arrays fabricated by direct synthesis ofoligonucleotides on a glass surface. Probe/Gene Arrays:Oligonucleotides, usually 25 mers, are directly synthesized onto a glasswafer by a combination of semiconductor-based photolithography and solidphase chemical synthesis technologies. Each array contains up to 400,000different oligos and each oligo is present in millions of copies. Sinceoligonucleotide probes are synthesized in known locations on the array,the hybridization patterns and signal intensities can be interpreted interms of gene identity and relative expression levels by the AffymetrixMicroarray Suite software. Each gene is represented on the array by aseries of different oligonucleotide probes. Each probe pair consists ofa perfect match oligonucleotide and a mismatch oligonucleotide. Theperfect match probe has a sequence exactly complimentary to theparticular gene and thus measures the expression of the gene. Themismatch probe differs from the perfect match probe by a single basesubstitution at the center base position, disturbing the binding of thetarget gene transcript. This helps to determine the background andnonspecific hybridization that contributes to the signal measured forthe perfect match oligo. The Microarray Suite software subtracts thehybridization intensities of the mismatch probes from those of theperfect match probes to determine the absolute or specific intensityvalue for each probe set. Probes are chosen based on current informationfrom GenBank® and other nucleotide repositories. The sequences arebelieved to recognize unique regions of the 3′ end of the gene. AGeneChip® Hybridization Oven (“rotisserie” oven) is used to carry outthe hybridization of up to 64 arrays at one time. The fluidics stationperforms washing and staining of the probe arrays. It is completelyautomated and contains four modules, with each module holding one probearray. Each module is controlled independently through Microarray Suitesoftware using preprogrammed fluidics protocols. The scanner is aconfocal laser fluorescence scanner which measures fluorescenceintensity emitted by the labeled cRNA bound to the probe arrays. Thecomputer workstation with Microarray Suite software controls thefluidics station and the scanner. Microarray Suite software can controlup to eight fluidics stations using preprogrammed hybridization, wash,and stain protocols for the probe array. The software also acquires andconverts hybridization intensity data into a presence/absence call foreach gene using appropriate algorithms. Finally, the software detectschanges in gene expression between experiments by comparison analysisand formats the output into .txt files, which can be used with othersoftware programs for further data analysis.

In some embodiments, the treatment is for a cancer selected from thegroup consisting of colorectal cancer, lung cancer, ovarian cancer,pituitary cancer, pancreatic cancer, mammary fibroadenoma, prostatecancer, head and neck squamous cell carcinoma, soft tissue sarcoma,breast cancer, neuroblastomas, melanoma, breast carcinoma, gastriccancer, colorectal cancer (CRC), epithelial carcinomas, brain cancer,endometrial cancer, testis cancer, cholangiocarcinoma, gallbladdercarcinoma, and hepatocellular carcinoma.

Biological samples are described herein, e.g., in the definition ofBiological Sample. In some embodiment, the biological sample is serum orof a tumor.

Articles of Manufacture

In another aspect of the invention, an article of manufacture containingmaterials useful for the treatment, prevention and/or diagnosis of thedisorders described above is provided. The article of manufacturecomprises a container and a label or package insert on or associatedwith the container. Suitable containers include, for example, bottles,vials, syringes, etc. The containers may be formed from a variety ofmaterials such as glass or plastic. The container holds a compositionwhich is by itself or when combined with another composition(s)effective for treating, preventing and/or diagnosing the condition andmay have a sterile access port (for example the container may be anintravenous solution bag or a vial having a stopper pierceable by ahypodermic injection needle). At least one active agent in thecomposition is an antibody of the invention. The label or package insertindicates that the composition is used for treating the condition ofchoice, such as cancer. Moreover, the article of manufacture maycomprise (a) a first container with a composition contained therein,wherein the composition comprises an antibody of the invention; and (b)a second container with a composition contained therein. The article ofmanufacture in this embodiment of the invention may further comprise apackage insert indicating that the first and second antibodycompositions can be used to treat a particular condition, e.g. cancer.Alternatively, or additionally, the article of manufacture may furthercomprise a second (or third) container comprising apharmaceutically-acceptable buffer, such as bacteriostatic water forinjection (BWFI), phosphate-buffered saline, Ringer's solution anddextrose solution. It may further include other materials desirable froma commercial and user standpoint, including other buffers, diluents,filters, needles, and syringes.

The following are examples of the methods and compositions of theinvention. It is understood that various other embodiments may bepracticed, given the general description provided above.

EXAMPLES

Commercially available reagents referred to in the Examples were usedaccording to manufacturer's instructions unless otherwise indicated.

Example 1 Generation of Humanized mu4F11 Antibodies

This example demonstrates the humanization of the murine antibody 4F11(mu4F11) directed against EGFL7. Residue numbers are according to Kabat(Kabat et al., Sequences of proteins of immunological interest, 5th Ed.,Public Health Service, National Institutes of Health, Bethesda, Md.(1991)). Single letter amino acid abbreviations are used.

Materials and Methods

Full length human EGFL7 and a truncated form of human EGFL7 (residues1-182) containing the EMI and 2 EGF domains (lacking the 2 coiled-coileddomains) were expressed in CHO cells and purified by conventional means(FIG. 1). Peptides containing the 4F11 epitope on EGFL7 called p2(RPRYACCPGWKRT; SEQ ID NO: 5) and EMI2 (PARPRYACCPGWKRTSGLPGACGAAICQPP;SEQ ID NO: 4) were made synthetically.

A hybridoma expressing the murine antibody 4F11 was obtained byimmunizing Egfl7 knockout mice with recombinant full length human EGFL7protein expressed in E. coli and refolded. Antibodies were screened byELISA using recombinant human or murine EGFL7 coated plates. A panel offunction blocking antibodies were identified by their ability to blockHUVEC adhesion to EGFL7 coated plates. Several antibodies wereidentified as cross-species function blocking antibodies, including onedesignated 4F11 (see co-owned International Patent Application WO2007/106915, filed 16 Mar. 2007 and published 20 Sep. 2007).

Cloning of Murine 4F11 Variable Domains and Generation of a Chimeric4F11 Antibody

Total RNA was extracted from hybridoma cells producing 4F11 usingstandard methods. The variable light (VL) and variable heavy (VH)domains were amplified using RT-PCR with degenerate primers to the heavyand light chains. The forward primers were specific for the N-terminalamino acid sequence of the VL and VH regions. Respectively, the LC andHC reverse primers were designed to anneal to a region in the constantlight (CL) and constant heavy domain 1 (CH1), which are highly conservedacross species. Amplified VL and VH were cloned into mammalianexpression vectors to generate a chimeric antibody ch4F11. Thepolynucleotide sequence of the inserts was determined using routinesequencing methods.

Direct Hypervariable Region Grafts onto Acceptor Human ConsensusFramework

The phagemid used for this work is a monovalent Fab-g3 display vectorand consists of 2 open reading frames under control of a single phoApromoter. The first open reading frame consists of the stII signalsequence fused to the VL and CH1 domains of the acceptor light chain andthe second consists of the stII signal sequence fused to the VH and CH1domains of the acceptor heavy chain followed by the minor phage coatprotein P3.

To make the CDR grafts, hypervariable regions from mu4F11 were graftedinto the huKI and huIII consensus acceptor frameworks to generate thedirect CDR-graft (4F11.v1) (FIGS. 2 and 3). In the VL domain thefollowing regions were grafted to the human consensus acceptor:positions 24-34 (L1; SEQ ID NO: 31), 50-56 (L2; SEQ ID NO: 32) and 89-97(L3; SEQ ID NO: 33). In the VH domain, positions 26-35 (H1; SEQ ID NO:34), 49-65 (H2; SEQ ID NO: 35) and 95-102 (H3; SEQ ID NO: 36) weregrafted. MacCallum et al. (MacCallum et al. J. Mol. Biol. 262: 732-745(1996)) have analyzed antibody and antigen complex crystal structuresand found position 49 of the heavy chain to be part of the contactregion thus it seems reasonable to include this position in thedefinition of CDR-H2 when humanizing antibodies.

4F11.v1 was generated by Kunkel mutagenesis as both a Fab displayed onphage and as an IgG using separate oligonucleotides for eachhypervariable region. Correct clones were identified by DNA sequencing.

Framework Toggle

To identify framework positions important for binding, a frameworktoggle phage library was generated to offer either the murine or humanamino acid at position 4 in VL, and positions 2, 48, 69, 71, 73, 75, 76,78 and 91 in VH. These positions were diversified as outlined in FIG. 4,by Kunkel mutagenesis using 5 oligonucleotides to mutate 4F11.v1 thatwas used as a template.

Randomization of the Hypervariable Regions

Sequence diversity was introduced at positions in the hypervariableregions using Kunkel mutagenesis. To generate a single position library(SPL), each position in each hypervariable region was individuallyrandomized to all possible 20 amino acids using oligonucleotidesencoding NNS. This resulted in 76 sub-libraries, each having a diversityof 20 that were combined into a pooled “single position library” (SPL)encompassing variants with a single mutation located within one of thehypervariable regions. The six templates used for mutagenesis had onestop codon (TAA) in the middle of CDR L1, L2, L3 H1, H2 or H3 to avoidreselecting the wild type sequence. When generating the SPL, theoligonucleotides used to introduce diversity also repaired the stopcodon in the corresponding template.

For the limited libraries, 4 oligonucleotides were incorporatedsimultaneously which repaired the stop codons (TAA) and introduced NNSat positions 53 and 54 in CDR-L2, 29 in CDR-H1, 52 in CDR-H2 and 98 inCDR-H3.

Generation of Phage Libraries

Oligonucleotides designed to introduce diversity into frameworkpositions or hypervariable regions as outlined above, werephosphorylated separately in 20 μl reactions containing 660 ng ofoligonucleotide, 50 mM Tris pH 7.5, 10 mM MgCl₂, 1 mM ATP, 20 mM DTT,and 5 U polynucleotide kinase for 1 h at 37° C.

To generate the framework toggle or limited libraries all phosphorylatedoligonucleotides directed to introduce diversity were addedsimultaneously to the mutagenesis reaction. For the SPL, 76 individualKunkel mutagenesis reactions were performed in a 96-well PCR plate. Fromthe phosphorylated oligonucleotides reactions (above), 2 μl was added to300 ng Kunkel template containing the corresponding stop codon in 50 mMTris pH 7.5, 10 mM MgCl₂ in a final volume of 10.11. The mixture wasannealed at 90° C. for 2 min, 50° C. for 5 min and then cooled on ice.The annealed template was then filled in by adding 0.5 μl 10 mM ATP, 0.5μl 10 mM dNTPs (10 mM each of dATP, dCTP, dGTP and dTTP), 1 μl 100 mMDTT, 1 μl 10×TM buffer (0.5 M Tris pH 7.5, 0.1 M MgCl₂), 80 U T4 ligase,and 4 U T7 polymerase in a total volume of 20 μl for 2 h at roomtemperature. These filled-in and ligated products were then eachtransformed into XL1-Blue cells, grown in 0.5 ml of 2YT containing 5μg/ml of tetracycline and M13/KO7 helper phage (MOI 10) for 2 hr at 37°C. and then pooled and transferred to 500 ml 2YT containing 50 μg/mlcarbenicillin and grown 16 h at 37° C.

Phage Selections

Multiple forms of antigen were used for phage selections. Full length ortruncated EGFL7 (5 μg/ml) were immobilized in 50 mM sodium bicarbonatepH 9.6 on MaxiSorp™ microtiter plates (Nunc) overnight at 4° C. EMI2 andp2 peptides were also biotinylated either through their free cysteine(using maleimide PEO₂-biotin; Pierce) or through the free amine on theiramino terminus (using NHS-LC-biotin, Pierce). For biotinylationreactions, a 2-fold molar excess of biotin reagent was used in PBS.Biotinylated EMI2 and p2 peptides were captured on NeutrAvidin® (2μg/ml) that had been immobilized in 50 mM sodium bicarbonate pH 9.6 onMaxiSorp™ microtiter plates (Nunc) overnight at 4° C. All plates wereblocked for at least 1 h using Blocker™ Casein (Pierce).

Phage were harvested from the culture supernatant and suspended in PBScontaining 5% powdered milk and 0.05% Tween™20 (PBSBT). Followingaddition of the phage library and a 1 hr incubation, microtiter wellswere washed extensively with PBS containing 0.05% Tween™20 (PBST) andbound phage were eluted by incubating the wells with 20 mM HCl, 500 mMKCl for 30 min. Eluted phage were neutralized with 1 M Tris, pH 8 andamplified using XL1-Blue cells and M13/KO7 helper phage and grownovernight at 37° C. in 2YT, 50 μg/ml carbenicillin. The titers of phageeluted from a target containing well were compared to titers of phagerecovered from a non-target containing well to assess enrichment.

Selection stringency was increased by both capturing phage that bound todecreasing concentrations of biotinylated p2 peptide in solutionfollowed by capture on NeutrAvidin® for 10 min (on rate selection) andby increasing the washing time and temperature to allow weak bindingphage to be washed away (off rate selection).

IgG Production

For screening purposes, IgG variants were initially produced in 293cells. Vectors coding for VL and VH (25 μg) were transfected into 293cells using the FuGENE® system. 5001 of FuGENE® was mixed with 4.5 ml ofDMEM media containing no FBS and incubated at room temperature for 5min. Each chain (25.1 g) was added to this mixture and incubated at roomtemperature for 20 min and then transferred to five T-150 flasks fortransfection overnight at 37° C. in 5% CO₂. The following day the mediacontaining the transfection mixture was removed and replaced with 23 mlPS04 media with 0.1 ml/L trace elements (A0934) and 10 mg/L insulin(A0940). Cells were incubated for an additional 5 days after which themedia was harvested at 1000 rpm for 5 min and sterile filtered using a0.22 μm low protein-binding filter. Samples could be stored at 4° C.after addition of 2.5 ml 0.1% PMSF for every 125 ml of media.

Affinity Determinations

Affinity determinations were performed by surface plasmon resonanceusing a BIAcore™-2000. Truncated EGFL7 or p2 peptide was immobilized(approximately 50-200 RU) in 10 mM sodium acetate pH 4.8 on a CM5 sensorchip. Purified IgG variants were injected (using a 2-fold serialdilution of 0.5 to 1000 nM in PBST) at a flow rate of 30 L/min. Eachsample was analyzed with 3-minute association and 3.5-minutedisassociation. After each injection the chip was regenerated using 10mM glycine pH 1.7.

Binding response was corrected by subtracting a control flow cell fromIgG variant flow cells. A 1:1 Languir model of simultaneous fitting ofk_(on) and k_(off) was used for kinetics analysis.

Cell Adhesion Assay

Mouse EGFL7 (mEGFL7-CB-His) or human EGFL7 (EGFL7-CB-His) were coated onmicrotiter plates at 5 μg/ml in sodium carbonate buffer O/N at 4° C.then blocked with 1% BSA in PBS. Anti-EGFL7 antibodies were added (0.01g/ml to 100 μg/ml), followed by the addition of 20,000 Human UmbilicalVein Endothelial Cells (HUVEC)/well in appropriate cell growth medium(EGM Lonza). Control cells were seeded in wells without antibody tocalculate 100% of seeded cells. Each antibody concentration was testedin triplicate. The plates were spun down for 5 min at 140 g tosynchronize contact of cells with substrate and then incubated in CO₂incubator for 30 min and washed 3 times with PBS. Cells that adhered tothe plates were counted using CyQUANT® buffer (Molecular Probes) andcalculated as percent of the total cells plated. The percentages ofcells that bound to the plate were plotted against the concentrations ofeach antibody.

Results and Discussion

Humanization of 4F11

The human acceptor framework used for humanization of mu4F11 is based onthe consensus human kappa I VL domain and the consensus human subgroupIII VH domain. Each complimentarity determining region (CDR) for mu4F11was identified and grafted into the human acceptor framework to generatea CDR graft (4F11.v1) that could be displayed as an Fab on phage (FIGS.2 and 3).

Antigen Evaluation for Phage Selection

The 4F11 epitope on EGFL7 was mapped to the second EMI domain and morespecifically to peptide p2 using a competition Western blot analysis(FIGS. 1 and 5). Phage displaying 4F11.v1 bound to immobilized fulllength and truncated EGFL7, but significant non-specific phage bindingwas also observed using a control phage (FIG. 6). For this reason, thep2 and EMI2 peptides that block 4F11 binding to truncated EGFL7 wereused for phage selections. The peptides were biotinylated either throughtheir free cysteine to generate p2S and EMI2c (using maleimidePEO₂-biotin; Pierce) or through the free amine on their amino terminusto generate p2N and EMI2.n (using NHS-LC-biotin, Pierce). To assessbinding, biotinylated peptides were captured in microtiter wells coatedwith NeutrAvidin®. Phage displaying 4F11.v1 were used to assess bindingto captured biotinylated EMI2 and p2 peptides. 4F11.v1 phage bound tobest to p2S (FIG. 7). The amount of phage captured was greatest when aconcentration of 50 nM biotinylated peptide was used for binding to theNeutrAvidin® coated well.

Screening Framework Positions

The framework toggle library was panned for 4 rounds of selection onimmobilized biotinylated p2S peptide. DNA sequence analysis of 96 clonesfrom the last round was used to evaluate the amino acid importance,based on abundance, at each toggled position (FIG. 8). Amino acidabundance prior to and after 4 rounds of selection suggested thereplacement of L78 with Thr (L78T) or Val (L78V) might lead to improvedbinding.

Screening CDR Positions

In order to identify further improvements, Single Position Librarieswere generated using 3 frameworks: the initial CDR graft (4F11.v1),4F11.v1 with L78T (4F11.v2), and 4F11.v1 with L78V (4F11.v3). For eachSPL, each position in each CDR was individually randomized to allpossible amino acids (a total of 76 libraries, each containing 20members, pooled into one SPL for each framework). Six 4F11.v1 DNAtemplates (containing stop codons in the appropriate CDRs) were used togenerate the three SPLs. The framework change at positions 78 in VH wasintroduced during SPL generation by using mutagenic oligonucleotidescoding for the appropriate framework change (L78V or L78V). Thus,framework and individual CDR positions were mutated simultaneously. TheSPLs were panned on soluble p2S peptide that was captured usingimmobilized NeutrAvidin® as outlined in Table 1:

TABLE 1 SPL Phage Selection Conditions Kon Selection Binding KoffSelection Antigen Time Excess Peptide Capture Round 1 Immobilized 1 hourNone — p2S (50 nM on NeutrAvidin ®) Round 2 Immobilized 1 hour None —p2S (50 nM on NeurAvidin) Round 3 20 nM p2S in 30 min 3 hours 10 minsolution Round 4 5 nM p2S in 30 min 4.5 hours; 37° C. 10 min solutionRound 5 10 nM p2S in 20 min  70 hours; 37° C. 10 min solutionSelection stringency was gradually increased by decreasing theconcentration of p2S peptide, reducing the time allowed for binding andincreasing the wash time and temperature. The highest phage recoveryduring the last 3 rounds of selection was observed with SPLs based on4F11.v2 and 4F11.v3.

Clones from the last round were picked for DNA sequence analysis.Individual sequence changes were identified in each CDR (FIG. 9). Themost abundant SPL clones had changes in VL at position N53Y in CDR-L2.Changes that appeared frequently and in more than one SPL wereincorporated into 4F11.v3. These variants (.v4 through .v12), the4F11-graft (.v1) and changes to the VH framework (4F11.v2 and 4F11.v3),were expressed as IgG, purified and tested for binding to immobilizedp2S by Biacore and using the Cell Adhesion Assay (Table 2). The weakerinhibition of cell adhesion observed for 4F11.v6 and 4F11.v10 comparedto mu4F11 indicated further affinity improvements were desirable.

TABLE 2 Humanized 4F11 Variants Expressed as IgG Hu4F11 Binding to p2S(Biacore ™) Cell Adhesion Assay Variant Light Chain Heavy Chain ka(1/Ms) kd (1/s) KD (nM) Variant/ch4F11 (fold) chimera 2.21E+05 7.51E−4 3.44 1.00 .v1 Graft Graft 3.42E+04 3.31E−03 96.8 .v2 Graft Graft + 78T5.35E+04 2.91E−03 54.4 .v3 Graft Graft + 78V 8.45E+04 2.92E−03 34.6 .v4Graft + L1: D28R Graft + 78V 2.31E+05 3.14E−03 13.6 .v5 Graft + L1: M33VGraft + 78V 7.11E+04 2.42E−03 34.0 .v6 Graft + L2: N53Y Graft + 78V1.23E+05 2.40E−03 19.5 4.01 .v7 Graft + L2: L54R Graft + 78V ND .v8Graft + L3: Y96F Graft + 78V ND .v9 Graft Graft + 78V + 2.64E+052.30E−03 9.0 H1: F29R .v10 Graft + L2: N53Y Graft + 78V + 7.20E+041.97E−03 27.4 4.38 H3: S98Y .v11 Graft Graft + 78V + ND H3: S98Y .v12Graft Graft + 78V + 1.96E+05 2.18E−03 11.1 H2: T52aI

Reassessment of Framework Positions

Additional framework changes were incorporated in sets. Variants wereexpressed as IgG (variants 13 through 16) and tested by Biacore™ asoutlined in Table 3:

TABLE 3 Humanized 4F11 Framework Variants Expressed as IgG Hu4F11 LightHeavy Binding to p2S (Biacore ™) Variant Chain Chain ka (1/Ms) kd (1/s)KD (nM) .v13 Graft + Graft + 1.49E+05 1.86E−03 12.5 M4L R71L, L78A .v14Graft + Graft + 1.41E+05 9.84E−04 7.0 M4L V2I, V48M, I69F, R71L, N73T,K75A, N76S, L78A, Y91F .v15 Graft Graft + 9.05E+04 2.76E−03 30.5 R71L,L78A .v16 Graft Graft + 9.81E+04 1.65E−03 16.8 V2I, V48M, I69F, R71L,N73T, K75A, N76S, L78A, Y91F ch4F11 2.15E+05 7.92E−04 3.7Of these, 4F11.v14 had the best affinity relative to mu4F11.

Limited Libraries

Two limited libraries were generated based on 4F11.v13 as a template.Library 1 contained the same framework changes as 4F11.V13 (LC:M4L andHC: R71L, L78A) while library 2 contained 2 additional changes in theheavy chain: N76S and Y91F (FIGS. 10 and 11). CDR changes in L1 and L3(D28S and D94E) were also incorporated into both libraries.Diversification was limited to positions where changes had beenpreviously observed following selection of the SPLs (FIGS. 10 and 11).These positions (53 and 54 in the light chain and 29, 52, 98 in theheavy chain) were diversified to include all twenty amino acids andpanned against immobilized p2S peptide that was captured usingimmobilized NeutrAvidin as outlined in Table 4:

TABLE 4 Limited Library Phage Selection Conditions Kon Selection BindingKoff Selection Antigen Time Excess Peptide Capture Round 1 Immobilized 1hour None — b-p2S (50 nM on NeutrAvidin ®) Round 2 Immobilized 1 hourNone — b-p2S (50 nM on NeurAvidin ®) Round 3 50 nM b-p2S in 60 min 30min, r.t. 10 min  solution Round 4 10 nM b-p2S in 30 min 1 hr; 37° C. 5min solution Round 5 10 nM b-p2S in 15 min 2 hr; 37° C. 5 min solution

The preference for different amino acid residues at the randomizedpositions for each library is plotted in FIG. 12. In light chain, bothlibraries preferentially selected 53Y and 54R, while in the heavy chain,there was a preference for 29F and 52T. In CDR-H3 of the heavy chain, 3amino acids were selected at position 98 (98Y, 98H, and 98R) in bothlibraries. To identify the best combination of these changes, variants17 through 26 (Table 5) were constructed, expressed and characterized asIgG. Several variants had affinities as good or better than ch4F11.Variants were further characterized in the cell migration assay usinghuman or mouse EGFL7 (Table 5 and FIGS. 13 and 14).

TABLE 5 Humanized 4F11 Variants Expressed as IgG Binding to p2S CellAdhesion Assay Light Chain Heavy Chain (Biacore ™) (human EGFL7) Hu4F11Position Position VH Framework Fold change in KD Variant/ch4F11 Variant53 54 29 52 98 used (variant/chimera) (fold) ch4F11 N L F T S 1 1.00.v17 Y R F T Y Library 1 0.93 0.86 .v18 Y R F T R Library 1 1.81 1.86.v19 Y R G T R Library 1 1.43 12.87 .v20 Y R F T H Library 1 1.79 0.70.v21 Y L R T R Library 1 1.31 3.12 .v22 Y R F T Y Library 2 1 0.81 .v23Y R F T R Library 2 3.88 nd .v24 Y R G T R Library 2 0.48 2.52 .v25 Y RF T H Library 2 0.56 1.82 .v26 Y L R T R Library 2 0.66 1.38

The VL and VH domains from hu4F11.v17 and 4F11.v22 compared to mu4F11and 4F11.v1 are shown in FIGS. 15 and 16, respectively.

Example 2 Generation of Humanized mu18F7 Antibodies

This example demonstrates the humanization of the murine antibody 18F7(mu18F7) directed against EGFL7. Residue numbers are according to Kabat(Kabat et al., Sequences of proteins of immunological interest, 5th Ed.,Public Health Service, National Institutes of Health, Bethesda, Md.(1991)). Single letter amino acid abbreviations are used.

Materials and Methods

Full length human EGFL7 and a truncated form of human EGFL7 (residues1-182) containing the EMI and 2 EGF domains (lacking the 2 coiled-coileddomains) were expressed in CHO cells and purified by conventional means(FIG. 1). Peptides containing the 18F7 epitope on EGFL7 called p5(RACSTYRTIYRTA; SEQ ID NO: 7) and EMI1 (LTTCDGHRACSTYRTIYRTAYRRSPG; SEQID NO: 3) were made synthetically.

A hybridoma expressing the murine antibody 18F7 was obtained byimmunizing Egfl7 knockout mice with recombinant full length human EGFL7protein expressed in E. coli and refolded. Antibodies were screened byELISA using recombinant human or murine EGFL7 coated plates. A panel offunction blocking antibodies were identified by their ability to blockHUVEC adhesion to EGFL7 coated plates. Several antibodies wereidentified as cross-species function blocking antibodies, including onedesignated 18F7 (see co-owned International Patent Application WO2007/106915, filed 16 Mar. 2007 and published 20 Sep. 2007).

Cloning of Murine 18F7 Variable Domains and Generation of a Chimeric18F7 Antibody

Total RNA was extracted from hybridoma cells producing 18F7 usingstandard methods. The variable light (VL) and variable heavy (VH)domains were amplified using RT-PCR with degenerate primers to the heavyand light chains. The forward primers were specific for the N-terminalamino acid sequence of the VL and VH regions. Respectively, the LC andHC reverse primers were designed to anneal to a region in the constantlight (CL) and constant heavy domain 1 (CH1), which are highly conservedacross species. Amplified VL and VH were cloned into mammalianexpression vectors to generate a chimeric antibody ch18F7. Thepolynucleotide sequence of the inserts was determined using routinesequencing methods.

Direct Hypervariable Region Grafts onto the Acceptor Human ConsensusFramework

The phagemid used for this work is a monovalent Fab-g3 display vectorand consists of 2 open reading frames under control of a single phoApromoter. The first open reading frame consists of the stII signalsequence fused to the VL and CH1 domains of the acceptor light chain andthe second consists of the stII signal sequence fused to the VH and CH1domains of the acceptor heavy chain followed by the minor phage coatprotein P3.

To make the CDR grafts, hypervariable regions from mu18F7 were graftedinto the huKI and huIII consensus acceptor frameworks to generate thedirect CDR-graft (18F7-graft) (FIGS. 17 and 18). In the VL domain thefollowing regions were grafted to the human consensus acceptor:positions 24-34 (L1; SEQ ID NO: 100), 50-56 (L2; SEQ ID NO: 101) and89-97 (L3; SEQ ID NO: 102). In the VH domain, positions 26-35 (H1; SEQID NO: 103), 49-65 (H2; SEQ ID NO: 104) and 95-102 (H3; SEQ ID NO: 105)were grafted. MacCallum et al. (MacCallum et al. J. Mol. Biol. 262:732-745 (1996)) have analyzed antibody and antigen complex crystalstructures and found position 49 of the heavy chain to be part of thecontact region thus it seems reasonable to include this position in thedefinition of CDR-H2 when humanizing antibodies.

The 18F7-graft was generated by Kunkel mutagenesis as both a Fabdisplayed on phage and as an IgG using separate oligonucleotides foreach hypervariable region. Correct clones were identified by DNAsequencing.

Framework Toggle

To identify framework positions important for binding, a frameworktoggle phage library was generated to offer either the murine or humanamino acid at positions 87 in VL, and positions 48, 67, 69, 71, 73, 75,76, 78 and 80 in VH. These positions were diversified as outlined inFIG. 19, by Kunkel mutagenesis using 3 oligonucleotides to mutate the18F7-graft that was used as a template.

Randomization of the Hypervariable Regions

Full sequence diversity was introduced separately at each position inthe hypervariable regions of the 18F7-graft using Kunkel mutagenesis togenerate single position libraries that were pooled together. Eachposition in each hypervariable region of 18F7-graft was fully randomizedto all possible 20 amino acids using oligonucleotides encoding NNS atthe respective positions. Multiple libraries were made each consistingof 20 members having a single position located within one of thehypervariable regions fully randomized. To cover each position in thehypervariable regions, 76 libraries of this type were generated andcombined into a pooled “single position library” (SPL) encompassingsingle mutations located throughout each hypervariable position. A stopcodon (TAA) was introduced in the middle of each CDR to avoidreselecting the wild type CDR grafted sequence. This was accomplished byKunkel mutagenesis and resulted in 6 different templates for the18F7-graft—each with a stop codon introduced into a different CDR. Whengenerating the library, the oligonucleotides used to introduce diversityalso repaired the stop codon in the corresponding template.

Generation of Phage Libraries

Oligonucleotides designed to introduce diversity into frameworkpositions or each hypervariable region as outlined above, werephosphorylated separately in 20.11 reactions containing 660 ng ofoligonucleotide, 50 mM Tris pH 7.5, 10 mM MgCl₂, 1 mM ATP, 20 mM DTT,and 5 U polynucleotide kinase for 1 h at 37° C.

To generate the framework toggle library all 3 phosphorylatedoligonucleotides directed to introduce diversity were addedsimultaneously to the mutagenesis reaction. For the SPL, 76 individualKunkel mutagenesis reactions were performed in a 96-well PCR plate. Fromthe phosphorylated oligonucleotides reactions (above), 2 μl was added to300 ng Kunkel template containing the corresponding stop codon in 50 mMTris pH 7.5, 10 mM MgCl₂ in a final volume of 10 μl. The mixture wasannealed at 90° C. for 2 min, 50° C. for 5 min and then cooled on ice.The annealed template was then filled in by adding 0.5 μl 10 mM ATP, 0.5μl 10 mM dNTPs (10 mM each of dATP, dCTP, dGTP and dTTP), 1 μl 100 mMDTT, 1 μl 10×TM buffer (0.5 M Tris pH 7.5, 0.1 M MgCl₂), 80 U T4 ligase,and 4 U T7 polymerase in a total volume of 20 μl for 2 h at roomtemperature. These filled-in and ligated products were then eachtransformed into XL1-Blue cells, grown in 0.5 ml of 2YT containing 5μg/ml of tetracycline and M13/KO7 helper phage (MOI 10) for 2 hr at 37°C. and then pooled and transferred to 500 ml 2YT containing 50 μg/mlcarbenicillin and grown 16 h at 37° C.

Phage Selections

Multiple forms of antigen were used for phage selections. Full length ortruncated EGFL7 (5 μg/ml) were immobilized in 50 mM sodium bicarbonatepH 9.6 on MaxiSorp™ microtiter plates (Nunc) overnight at 4° C. EMI1 andp5 peptides were also biotinylated either through their free cysteine(using maleimide PEO₂-biotin; Pierce) or through the free amine on theiramino terminus (using NHS-LC-biotin, Pierce). For biotinylationreactions, a 2-fold molar excess of biotin reagent was used in PBS.Biotinylated EMI1 and p5 peptides were captured on NeutrAvidin® (2μg/ml) that had been immobilized in 50 mM sodium bicarbonate pH 9.6 onMaxiSorp™ microtiter plates (Nunc) overnight at 4° C. All plates wereblocked for at least 1 h using Blocker™ Casein (Pierce).

Phage were harvested from the culture supernatant and suspended in PBScontaining 5% powdered milk and 0.05% Tween™20 (PBSBT). Followingaddition of the phage library and a 1 hr incubation, microtiter wellswere washed extensively with PBS containing 0.05% Tween™20 (PBST) andbound phage were eluted by incubating the wells with 20 mM HCl, 500 mMKCl for 30 min. Eluted phage were neutralized with 1 M Tris, pH 8 andamplified using XL1-Blue cells and M13/KO7 helper phage and grownovernight at 37° C. in 2YT, 50 μg/ml carbenicillin. The titers of phageeluted from a target containing well were compared to titers of phagerecovered from a non-target containing well to assess enrichment.

Selection stringency was increased by both capturing phage that bound todecreasing concentrations of biotinylated p5 peptide in solutionfollowed by capture on NeutrAvidin® for 10 min (on rate selection) andby increasing the washing time and temperature to allow weak bindingphage to be washed away (off rate selection).

IgG Production

For screening purposes, IgG variants were initially produced in 293cells. Vectors coding for VL and VH (25 μg) were transfected into 293cells using the FuGENE® system. 5001 of FuGENE® was mixed with 4.5 ml ofDMEM media containing no FBS and incubated at room temperature for 5min. Each chain (25.1 g) was added to this mixture and incubated at roomtemperature for 20 min and then transferred to five T-150 flasks fortransfection overnight at 37° C. in 5% CO₂. The following day the mediacontaining the transfection mixture was removed and replaced with 23 mlPS04 media with 0.1 ml/L trace elements (A0934) and 10 mg/L insulin(A0940). Cells were incubated for an additional 5 days after which themedia was harvested at 1000 rpm for 5 min and sterile filtered using a0.22 μm low protein-binding filter. Samples could be stored at 4° C.after addition of 2.5 ml 0.1% PMSF for every 125 ml of media.

Affinity Determinations

Affinity determinations were performed by surface plasmon resonanceusing a BIAcore™-2000. Truncated EGFL7 or p5 peptide was immobilized(approximately 50-200 RU) in 10 mM sodium acetate pH 4.8 on a CM5 sensorchip. Purified IgG variants were injected (using a 2-fold serialdilution of 0.5 to 1000 nM in PBST) at a flow rate of 30 μL/min. Eachsample was analyzed with 3-minute association and 3.5-minutedisassociation. After each injection the chip was regenerated using 10mM glycine pH 1.7.

Binding response was corrected by subtracting a control flow cell fromIgG variant flow cells. A 1:1 Languir model of simultaneous fitting ofk_(on) and k_(off) was used for kinetics analysis.

Results and Discussion

Humanization of 18F7

The human acceptor framework used for humanization of mu18F7 is based onthe consensus human kappa I VL domain and the consensus human subgroupIII VH domain. Each CDR for mu18F7 was identified and grafted into thehuman acceptor framework to generate a CDR graft that could be displayedas an Fab on phage (FIGS. 17 and 18).

Antigen Evaluation for Phage Selection

The 18F7 epitope on EGFL7 was mapped to the first EMI domain and morespecifically to peptide p5 using a competition Western blot analysis(FIGS. 1 and 20). Phage displaying the 18F7-graft bound to immobilizedfull length and truncated EGFL7, but significant non-specific phagebinding was also observed using a control phage (FIG. 21). For thisreason, the p5 and EMI1 peptides that block 18F7 binding to truncatedEGFL7 were used for phage selections. The peptides were biotinylatedeither through their free cysteine to generate p5c and EMI1c (usingmaleimide PEO₂-biotin; Pierce) or through the free amine on their aminoterminus to generate p5n and EMI1n (using NHS-LC-biotin, Pierce). Toassess binding, biotinylated peptides were captured in microtiter wellscoated with NeutrAvidin®. Following 2 rounds of selection on immobilizedtruncated EGFL7, the framework toggle library phage pool was used toassess binding to captured biotinylated EMI1 and p5 peptides. The phagepool bound to p5n and EMI1n, but not to p5c or EMI1c (FIG. 22). Theamount of phage captured was greatest when a concentration of 50 nMbiotinylated peptide was used for binding to the NeutrAvidin® coatedwell.

After selection for 2 rounds against immobilized truncated EGFL7, theframework toggle library was further panned for 2 rounds of selection onimmobilized biotinylated p5n peptide. DNA sequence analysis of 96 clonesfrom the last round was used to evaluate the amino acid importance,based on abundance, at each toggled position (FIG. 23). Amino acidabundance prior to and after 4 rounds of selection suggested the changesN73K and L78A lead to improved binding. Although less prominent, L78Vand V48I also do so and L78V was further studied.

SPLs were explored in an effort to identify further improvements using 4frameworks derived from the framework toggle library results. The 4frameworks included the initial CDR graft (18F7-graft), 18F7-graft withN73K (18F7.v2), 18F7-graft with N73K and L78A (18F7.v3), and 18F7-graftwith N73K and L78V (18F7.v4). For each framework, an SPL was generatedwhere each position in each CDR was individually randomized to allpossible amino acids (a total of 76 libraries, each containing 20members, pooled into one SPL). Six 18F7-graft DNA templates (containingstop codons in the appropriate CDRs) were used to generate all fourSPLs. Framework changes at positions 73 and 78 in VH were introducedduring SPL generation by using mutagenic oligonucleotides coding for theappropriate framework changes. Thus, framework and individual CDRpositions were mutated simultaneously. The four SPLs were panned for 2rounds against immobilized truncated EGFL7 followed by 3 rounds ofselection on soluble biotinylated p5n peptide that was captured usingimmobilized NeutrAvidin® as outlined in Table 6:

TABLE 6 SPL Phage Selection Conditions Kon Selection Binding KoffSelection Antigen Time Excess Peptide Capture Round 1 Immobilized 1 hourNone — b-p5N (50 nM on NeutrAvidin ®) Round 2 Immobilized 1 hour None —b-p5N (50 nM on NeurAvidin ®) Round 3 20 nM b-p5N 30 min 3 hours 10 minRound 4 5 nM b-p5N 30 min 4.5 hours; 37° C. 10 min Round 5 10 nM b-p5N20 min  70 hours; 37° C. 10 minSelection stringency was gradually increased by decreasing theconcentration of biotinylated p5n peptide, reducing the time allowed forbinding and increasing the wash time and temperature. The highest phagerecovery during the last 3 rounds of selection was observed with SPLsbased on 18F7.v3 and 18F7.v4.

Clones from the last round were picked for DNA sequence analysis.Individual sequence changes were identified in each CDR (FIG. 24). Themost abundant SP library clones had changes in VL at position S89.Changes that appeared frequently and in more than one SP library wereincorporated into 18F7.v3. These variants (.v5 through .v10), the18F7-graft (.v1) and changes to the VH framework (.v2, .v3 and .v4),were expressed as IgG for further analysis by Biacore™ (Tables 7 and 8).

TABLE 7 18F7-graft Variants Expressed as IgG hu18F7grafted variantsLight Chain Heavy Chain .v1 Graft Graft .v2 Graft 73K .v3 Graft 73K &78A .v4 Graft 73K & 78V .v5 L2: F55G 73K & 78A .v6 L3: S89G 73K & 78A.v7 L3: S89A 73K & 78A .v8 L3: S89V 73K & 78A .v9 Graft 73K & 78A & H1:Y32K .v10 Graft 73K & 78A & H3: D100P

TABLE 8 Biacore ™ Analysis of 18F7-graft Variants Biacore Analysis of18F7 Variants Over mEGFL7-CB at 37 C. 37 C. over immobolized P5 ka(1/Ms/1e5) kd (1/s*1e4) KD (nM) ka (1/Ms/1e5) kd (1/s*1e4) KD (nM)Chimeric 18F7 n = 5 0.36 ± 0.16 0.96 ± 0.78 3.17 ± 3.48 Chimeric 18F7 n= 5 1.09 ± 0.30 5.44 ± 0.49 5.51 ± 2.46 18F7 V1 0.97 2.74 2.82 18F7 V13.17 20 6.3 18F7 V2 1.10 1.98 1.81 18F7 V2 4.58 11.9 2.59 18F7 V3 0.550.905 1.64 18F7 V3 2.03 8.58 4.22 18F7 V4 0.50 2.08 4.15 18F7 V4 1.8213.2 7.27 18F7 V5 0.73 1.17 1.61 18F7 V5 3.30 8.92 2.7 18F7 V6 0.500.204 0.408 18F7 V6 n = 3 1.21 ± 0.14 3.89 ± 0.71 3.21 ± 0.49 18F7 V70.70 0.958 1.38 18F7 V7 2.51 7.18 2.87 18F7 V8 0.98 1.99 2.04 18F7 V84.72 10.2 2.16 18F7 V9 0.59 0.932 1.58 18F7 V9 2.28 7.63 3.35 18F7 V101.60 1.95 1.22 18F7 V10 8.25 8.11 0.982 18F7 V6A n = 2 0.55 ± 0.01 4.04± 0.00 7.29 ± 0.17 18F7 V6A n = 2 3.73 ± 0.91 13.70 ± 1.41  3.74 ± 0.5218F7 V6B n = 2 0.79 ± 0.25 1.74 ± 1.75 2.68 ± 3.06 18F7 V6B n = 2 1.96 ±0.25 6.38 ± 1.82 3.22 ± 0.52 18F7 V6C n = 2 0.36 ± 0.06 0.81 ± 0.36 2.40± 1.42 18F7 V6C n = 2 1.24 ± 0.28 5.02 ± 0.31 4.13 ± 0.66 18F7 V6D 1.037.91 7.65 18F7 V6D n = 2 3.13 ± 1.89 23.25 ± 5.59  9.77 ± 7.69 18F7 V6E0.48 4.74 9.9 18F7 V6E 3.03 15.4 5.1 18F7 V6I 0.23 4.88 21.3 18F7 V6I1.90 31.6 16.7 18F7 V6J 0.21 0.164 6.8 18F7 V6J 1.08 6.07 5.6 18F7 V6K0.28 0.454 1.6 18F7 V6K 1.27 6.62 5.2Biacore™ analysis of these 10 variants indicated all bound quite well toimmobilized mEGFL7 or the p5 peptide. 18F7.v6 had the slowestdissociation rate (kd) and was effective in the HUVEC adhesion assay(FIG. 25).

Polishing of 18F7.v6

Potential iso-aspartic acid forming sites (Asn-Gly) in CDR-L1 (N28,G29)and CDR-H2 (N54, G55) in 18F7.v6 were eliminated by testing alternativeamino acids at these positions (Table 9).

TABLE 9 Variants Tested to Eliminate Potential Iso-aspartic Acid FormingSites hu18F7.v6 variants Light Chain (N28 & G29) Heavy Chain (N54 & G55).v6A L1: SG (SEQ ID NO: 243) .v6 (SEQ ID NO: 104) .v6B .v6 (SEQ ID NO:100) H2: SG (SEQ ID NO: 177) .v6C .v6 (SEQ ID NO: 100) H2: NS (SEQ IDNO: 247) .v6D L1: SG (SEQ ID NO: 243) H2: SG (SEQ ID NO: 177) .v6E L1:SG (SEQ ID NO: 243) H2: NS (SEQ ID NO: 247) .v6I L1: QG (SEQ ID NO: 244)H2: NS (SEQ ID NO: 247) .v6J L1: NS (SEQ ID NO: 245) H2: NS (SEQ ID NO:247) .v6K L1: NA (SEQ ID NO: 246) H2: NS (SEQ ID NO: 247)An SG sequence in H2 (.v6B and .v6D) expressed poorly, while thissequence in L1 (.v6A) increased the dissociation rate. In contrast, anNS sequence in H2 (.v6C) had little affect on the kinetics (Tables 8 and9). Of the other changes sampled in L1 in conjunction with H2:NS (.v6C),the changes NS (.v6J) and NA (.v6K) had a minimal affect on thedissociation rate (Table 8 and 9, FIG. 25). These changes can be used toimprove the stability of 18F7.v6 while still maintaining desiredbiological properties compared to murine 18F7 (FIGS. 25 and 26). The VLand VH domains from hu18F7.v6K are shown in FIGS. 27 and 28,respectively.

Example 3 Treatment of Tumor-Bearing Mice or Neonatal Mice withHumanized Anti-EGFL7 Antibody

We investigated the ability of humanized anti-EGFL7 antibodies of theinvention (alone and in combination with anti-VEGF therapy) to inhibitangiogenesis and/or tumor growth in a variety of models. We observedanti-EGFL7 antibodies enhance the efficacy of anti-VEGF therapy.

HRLN female nu/nu mice were injected subcutaneously with 1×10⁷ H1299human non-small cell lung cancer tumor cells and allowed to developtumors to 80-120 mm³. Tumor-bearing mice were then randomly separatedinto four groups (12 mice each) so that the average tumor size in eachgroup was 122 mm³. These mice were then treated as follows: Group 1:intraperitoneal (ip) injection of anti-VEGF antibody (B20-4.1;WO2005/012359 and WO2005/044853) once per week at 10 mg/kg; Group 2: ipinjection of a negative control antibody anti-ragweed IgG once per weekat 10 mg/kg and anti-EGFL7 antibody (hu18F7.v6K) twice per week at 10mg/kg; Group 3: ip injection of B20-4.1 once per week at 10 mg/kg andhu18F7.v6K twice per week at 10 mg/kg; Group 4: no treatment. Tumorswere measured twice per week with a caliper and tumor volumes werecalculated as (w²×l)/2 (w=tumor width in mm, l=tumor length in mm). Micewere euthanized when their tumors reached 1000 mm³ (defined as “micereached end point”). Group average tumor volumes+/−SEM were plottedagainst time until ≧50% of the mice reached end point. The data fromthis experiment showed that treatment with neither B20.4-1 norhu18F7.v6K alone significantly reduced tumor growth over untreatedcontrol, although treatment with hu18F7.v6K exhibited a trend towardreduced growth (FIG. 29). In contrast, treatment with both B20.4-1 andhu18F7.v6K significantly inhibited tumor growth (FIG. 29).

Balb-c nude mice were injected subcutaneously in the right flank with5×10⁶ HM7 carcinoma cells in 0.1 ml Matrigel™. When mean tumor sizereached 80-150 mm³, animals were separated into 4 groups of 10 mice eachso that the average tumor sizes in all the groups were roughly equal andtreated as follows: Group 1: ip injection of anti-ragweed IgG twice perweek at 5 mg/kg; Group 2: ip injection of B20-4.1.1 (PCT/US2008/013248)twice per week at 5 mg/kg; Group 3: ip injection of anti-EGFL7 antibody(hu18F7.v6k) twice per week at 10 mg/kg; Group 4: ip injection ofB20-4.1.1 twice per week at 5 mg/kg and hu18F7.v6k twice per week at 10mg/kg. Tumors were measured twice per week with a caliper and the widthand length recorded. Mice were euthanized when tumors were greater than1000 mm³ or when tumor growth or ulceration interfered with animalhealth. We observed that tumors in Groups 1 and 3 had similar growthrates, whereas tumors in Group 2 grew more slowly than those in Group 1and tumors in Group 4 exhibited a negative growth.

Balb-c nude mice were injected subcutaneously in the right flank withprimary human large cell lung cancer tumor explants (LXFL 1674). Theexperiment comprised a reference group (Group 1) dosed with human IgG(hIgG) and murine IgG (mIgG) control antibodies, Group 2 that receivedhu18F7.v6k and mIgG, Group 3 that received B20-4.1.1 and hIgG, and Group4 that received hu18F7.v6K and B20-4.1.1. All treatments were giventwice weekly ip with hu18F7.v6k (or hIgG) given at 10 mg/kg/dose fourhours prior to B20 (or mIgG) administered at 5 mg/kg/dose. Mice weresacrificed individually when tumor volume exceeded 2000 mm³. Groups wereevaluated for efficacy as long as more than 50% of Group 1 control micewere alive (day 14). Group size at the start of dosing was 10 micebearing one tumor of 5-10 mm in diameter each per mouse. The advantageof the combination therapy over the B20-4.1.1 monotherapy wasstatistically significant (FIG. 30).

We also tested the humanized anti-EGFL7 antibody hu18F7.v6k and itsparental antibody murine 18F7 in a murine neonatal organ angiogenesisassay. Newborn mice were injected with antibodies at days 1 and 3 afterbirth and organs were harvested on day 5. The vasculatures in multipleorgans were stained with a vascular endothelial cell marker CD31 andvascular densities were quantified. The groups were: Group 1 whichreceived 15 mg/ml anti-ragweed antibody (n=3/experiment), Group 2 whichreceived 5 mg/ml anti-VEGF antibody (G6.31; WO2005/012359 andWO2005/044853; n=3/experiment) and 10 mg/ml ragweed antibody, Group 3which received 5 mg/ml G6.31 and 10 mg/ml murine 18F7 (n=4/experiment),and Group 4 which received 5 mg/ml G6.31 and 10 mg/ml hu18F7.v6k(n=4/experiment). The pooled results from three independent experimentsare shown in FIG. 31, which demonstrated that the anti-VEGF antibodyG6.31 has significant anti-angiogenesis activity, and the combination ofG6.31 with either hu18F7.v6k or murine 18F7 significantly enhanced theactivity of G6.31. Similar anti-angiogenesis activities were observed inthe intestinal villus vasculature. These results confirm that hu18F7.v6kand murine 18F7 have similar anti-angiogenesis activities in this model.

Example 4 Inhibition of Tumor Perfusion and Permeability by Anti-EGFL7Antibodies in Human Subjects

We conducted dynamic contrast-magnetic resonance imaging (DCE-MRI)assessments on human subjects who had been administered with two cyclesof 3 mg/kg or mg/kg hu18F7.v6k to explore changes in tumor vasculaturein response to the antibody. DCE-MRI is an imaging modality that allowsfor the functional analysis of tumor microcirculation. Changes invascular parameters such as V_(e), the fractional extravascular andextracellular leakage volume, and K_(trans), the volume transferconstant, reflect changes in tumor perfusion and permability. Twobaseline pre-treatment scans were obtained approximately 5-7 days apart(but at least 24 hours apart) prior to dosing in Cycle 1 (for example,Day −1 and Day −7 relative to administration of antibody).Post-treatment scans were obtained on Day 15 of Cycle 1 and on Day 8 ofCycle 2 (±2 days to allow for scheduling difficulties). Evaluablemetastatic lesions had to measure ≧3 cm in the liver, or ≧2 cm elsewherein at least one dimension. In addition to DCE-MRI acquisition sequences,other MRI acquisition sequences, such as diffusion-weighted imaging andT1- and T2-weighted imaging were acquired during the same imageacquisition visit for each subject. As shown in Table 10, we observedthat treatment with anti-EGFL7 antibodies reduced K_(trans) in somesolid tumors by up to approximately 40%.

TABLE 10 Median K_(trans) Patent Identifier, liver tumor volume, andCycle 1, Cycle 2, hu18F7.v6k dosage Base 1 Base 2 Day 15 Day 8 3301, 82cc (3 mg/kg) ND 0.021 0.0171 ND 3503, 7 cc (15 mg/kg) ND 0.0542 0.04350.0327 3505, 11 cc (15 mg/kg) 0.0278 0.0288 0.0239 0.019 3505, 142 cc(15 mg/kg) 0.0239 0.022 0.0229 0.02 3902, 235 cc (3 mg/kg) 0.022 0.0190.02 0.022

What is claimed is:
 1. A method of enhancing efficacy of ananti-angiogenesis agent in a subject having a pathological conditionassociated with angiogenesis, the method comprising administering to anindividual in need of such treatment an effective amount of ananti-EGFL7 antibody, the antibody comprising the following hypervariableregion (HVR) sequences: (i) HVR-L1 comprising KX₁SX₂SX₃DYX₄GDSYX₅S,wherein X₁ is A or R; X₂ is H or Q; X₃ is G or V; X₄ is selected fromthe group consisting of D, L, R, S, and W; and X₅ is M or V (SEQ ID NO:210); (ii) HVR-L2 comprising GASX₁X₂EX₃, wherein X₁ is N or Y; X₂ isselected from the group consisting of L, R and Y; and X₃ is Q or S (SEQID NO: 211); (iii) HVR-L3 comprising QQNNEX₁PX₂T, wherein X₁ is D or E;and X₂ is F or Y (SEQ ID NO: 212); (iv) HVR-H1 comprisingGX₁X₂X₃X₄TYGX₅S, wherein X₁ is H or V; X₂ is R or T; X₃ is selected fromthe group consisting of F, G, R, and S; X₄ is selected from the groupconsisting of D, G, R, and T; and X₅ is M or Y (SEQ ID NO: 213); (v)HVR-H2 comprising GWINX₁X₂SGVPTX₃AX₄X₅X₆X₇X₈, wherein X₁ is selectedfrom the group consisting of I, M, T, and W; X₂ is H or R; X₃ isselected from group consisting of I, M, T, and Y; X₄ is D or H; X₅ isselected from group consisting of D, M and T; X₆ is F or Y; X₇ is K orS; and X₈ is G or R (SEQ ID NO: 214, and (vi) HVR-H3 comprisingAX₁LGSX₂AVDX₃, wherein X₁ is N or R; X₂ is selected from the groupconsisting of C, R, H, and Y; and X₃ is A or Y (SEQ ID NO: 215).
 2. Amethod of enhancing efficacy of an anti-angiogenesis agent in a subjecthaving a pathological condition associated with angiogenesis, the methodcomprising administering to an individual in need of such treatment aneffective amount of an anti-EGFL7 antibody, the antibody comprising thefollowing HVR sequences: HVR-L1 comprising an amino acid sequenceselected from SEQ ID NOs: 37-43, HVR-L2 comprising an amino acidsequence selected from the group consisting of SEQ ID NOs: 44-47, HVR-L3comprising the amino acid sequence SEQ ID NO: 48, HVR-H1 comprising anamino acid sequence selected from the group consisting of SEQ ID NOs:49-57, HVR-H2 comprising an amino acid sequence selected from the groupconsisting of SEQ ID NOs: 58-73, and HVR-H3 comprising an amino acidsequence selected from the group consisting of SEQ ID NOs: 74-77.
 3. Themethod of claim 1, wherein HVR-L1 comprises the amino acid sequenceKASQSVDYSGDSYMS (SEQ ID NO: 234), HVR-L2 comprises the amino acidsequence GASYRES (SEQ ID NO: 235), HVR-L3 comprises the amino acidsequence QQNNEEPYT (SEQ ID NO: 236), HVR-H1 comprises the amino acidsequence GHTFTTYGMS (SEQ ID NO: 34), HVR-H2 comprises the amino acidsequence GWINTHSGVPTYADDFKG (SEQ ID NO: 35), and HVR-H3 comprises theamino acid sequence ARLGSYAVDY (SEQ ID NO: 237).
 4. The method of claim1, wherein the heavy chain comprises the following framework sequences:FR-H1 comprises EX₁QLVESGGGLVQPGGSLRLSCAAS, wherein X₁ is I or V (SEQ IDNO: 216); FR-H2 comprises WVRQAPGKGLEWX₁, wherein X₁ is I, M, or V (SEQID NO: 217); FR-H3 comprises RFTX₁SX₂DX₃SX₄X₅TX₆YLQMNSLRAEDTAVYX₇CAR,wherein X₁ is F or I; X₂ is L or R; X₃ is N or T, X₄ is selected fromthe group consisting of A, E, K and T; X₅ is N or S; X₆ is selected fromthe group consisting of A, L, M, T and V; and X₇ is F or Y (SEQ ID NO:218); and FR-H4 comprises WGQGTLVTVSS (SEQ ID NO: 219).
 5. The method ofclaim 4, wherein the heavy chain comprises the following frameworksequences: FR-H1 comprises EVQLVESGGGLVQPGGSLRLSCAAS (SEQ ID NO: 197);FR-H2 comprises WVRQAPGKGLEWV (SEQ ID NO: 198); FR-H3 comprisesRFTISX₁DNSKNTX₂YLQMNSLRAEDTAVYYCAR, wherein X₁ L or R; X₂ is selectedfrom the group consisting of A, L, M, T and V (SEQ ID NO: 220); andFR-H4 comprises WGQGTLVTVSS (SEQ ID NO: 200).
 6. The method of claim 4,wherein the heavy chain comprises the following framework sequences:FR-H1 comprises EIQLVESGGGLVQPGGSLRLSCAAS (SEQ ID NO: 238); FR-H2comprises WVRQAPGKGLEWM (SEQ ID NO: 239); FR-H3 comprisesRFTISX₁DNSKSTX₂YLQMNSLRAEDTAVYFCAR, wherein X₁ L or R; X₂ is selectedfrom the group consisting of A, L, M, T and V (SEQ ID NO: 240); andFR-H4 comprises WGQGTLVTVSS (SEQ ID NO: 219).
 7. The method of claim 1,wherein the light chain comprises the following framework sequences:FR-L1 comprises DIQMTQSPSSLSASVGDRVTITC (SEQ ID NO: 201), FR-L2comprises WYQQKPGKAPKLLIY (SEQ ID NO: 202), FR-L3 comprisesGVPSRFSGSGSGTDFTLTISSLQPEDFATYYC (SEQ ID NO: 203), FR-L4 comprisesFGQGTKVEIK (SEQ ID NO: 221) or FGQGTKVEIKR (SEQ ID NO: 204).
 8. Themethod of claim 1, wherein the light chain comprises the variable domainsequence of 4F11.v17 as shown in FIG. 15 (SEQ ID NO: 82) or the variabledomain sequence of 4F11.v22 as shown in FIG. 15 (SEQ ID NO: 83).
 9. Themethod of claim 1, wherein the heavy chain comprises the variable domainsequence of 4F11.v17 as shown in FIG. 16 (SEQ ID NO: 84) or the variabledomain sequence of 4F11.v22 as shown in FIG. 16 (SEQ ID NO: 85).
 10. Themethod of claim 1, wherein the light chain comprises the variable domainsequence of 4F11.v17 as shown in FIG. 15 (SEQ ID NO: 82) and the heavychain comprises the variable domain sequence of 4F11.v17 as shown inFIG. 16 (SEQ ID NO: 84).
 11. The method of claim 1, wherein the lightchain comprises the variable domain sequence of 4F11.v22 as shown inFIG. 15 (SEQ ID NO: 83) and the heavy chain comprises the variabledomain sequence of 4F11.v22 as shown in FIG. 16 (SEQ ID NO: 85).
 12. Themethod of claim 1, wherein at least a portion of the framework sequenceis a human consensus framework sequence.
 13. The method of claim 12,comprising human κ subgroup 1 consensus framework sequence or heavychain human subgroup III consensus framework sequence.
 14. A method ofenhancing efficacy of an anti-angiogenesis agent in a subject having apathological condition associated with angiogenesis, the methodcomprising administering to an individual in need of such treatment aneffective amount of an anti-EGFL7 antibody, the antibody comprising avariable domain comprising the following HVR sequences: (i) HVR-L1comprising X₁X₂X₃X₄X₅X₆VX₇X₈X₉X₁₀ITYLX₁₁, wherein X₁ is selected fromthe group consisting of L, Q, R, S, and T; X₂ is selected from the groupconsisting of P, T, and W; X₃ is H or S; X₄ is D or Q; X₅ is G or S; X₆is L or V; X₇ is H or P; X₈ is selected from the group consisting of I,L, P, T, and Y; X₉ is selected from the group consisting of N, Q or S;X₁₀ is selected from the group consisting of A, G, and S; and X₁₁ is Gor H (SEQ ID NO: 222); (ii) HVR-L2 comprising RVSNX₁X₂S, wherein X₁ is Dor R; and X₂ is selected from the group consisting of A, G, F, I, and T(SEQ ID NO: 223); (iii) HVR-L3 comprising X₁QSX₂X₃VPLT, wherein X₁ isselected from the group consisting of A, G, I, K, L, N, T, and V; X₂ isC or T; and X₃ is F or H (SEQ ID NO: 224); (iv) HVR-H1 comprisingGYX₁X₂X₃DX₄YX₅N, wherein X₁ is N or T; X₂ is F or V; X₃ is selected fromthe group consisting of I, M, R, and S; X₄ is selected from the groupconsisting of Y, Q, and K; and X₅ is I or M (SEQ ID NO: 225); (v) HVR-H2comprising GDINX₁X₂X₃X₄X₅X₆HX₇X₈X₉X₁₀X₁₁X₁₂X₁₃, wherein X₁ is selectedfrom the group consisting of A, L, N, and P; X₂ is selected from thegroup consisting of D, L, and R; X₃ is selected from the groupconsisting of G, K, N, R, S, and Y; X₄ is G or S; X₅ is selected fromthe group consisting of G, I, K, R, S, T, and V; X₆ is selected from thegroup consisting of G, R, and T; X₇ is selected from the groupconsisting of I, V, L, and Y; X₈ is N or S; X₉ is selected from thegroup consisting of A, N, and Q; X₁₀ is K or V; X₁₁ is F or Q; X₁₂ is Kor T; and X₁₃ is selected from the group consisting of G, H, R, and S(SEQ ID NO: 226); and (vi) HVR-H3 comprising X₁REGVYHX₂YDDYAX₃DY,wherein X₁ is selected from the group consisting of A, N, and T; X₂ is Dor P; and X₃ is M or W (SEQ ID NO: 227).
 15. A method of enhancingefficacy of an anti-angiogenesis agent in a subject having apathological condition associated with angiogenesis, the methodcomprising administering to an individual in need of such treatment aneffective amount of an anti-EGFL7 antibody, the antibody comprising thefollowing HVR sequences: HVR-L1 comprising an amino acid sequenceselected from SEQ ID NOs: 106-124 and 243-246, HVR-L2 comprising anamino acid sequence selected from the group consisting of SEQ ID NOs:125-129, HVR-L3 comprising an amino acid sequence selected from thegroup consisting of SEQ ID NOs: 130-145, HVR-H1 comprising an amino acidsequence selected from the group consisting of SEQ ID NOs: 146-153,HVR-H2 comprising an amino acid sequence selected from the groupconsisting of SEQ ID NOs: 154-187 and 247, and HVR-H3 comprising anamino acid sequence selected from the group consisting of SEQ ID NOs:188-192.
 16. The method of claim 14, wherein HVR-L1 comprises the aminoacid sequence RTSQSLVHINAITYLH (SEQ ID NO: 241), HVR-L2 comprises theamino acid sequence RVSNRFS (SEQ ID NO: 101), HVR-L3 comprises the aminoacid sequence GQSTHVPLT (SEQ ID NO: 131), HVR-H1 comprises the aminoacid sequence GYTFIDYYMN (SEQ ID NO: 103), HVR-H2 comprises the aminoacid sequence GDINLDNSGTHYNQKFKG (SEQ ID NO: 242), and HVR-H3 comprisesthe amino acid sequence AREGVYHDYDDYAMDY (SEQ ID NO: 105).
 17. Themethod of claim 14, wherein the heavy chain comprises the followingframework sequences: FR-H1 comprises EVQLVESGGGLVQPGGSLRLSCAAS (SEQ IDNO: 197); FR-H2 comprises WVRQAPGKGLEWX₁, wherein X₁ is I or V (SEQ IDNO: 228); FR-H3 comprises RX₁TX₂SX₃DX₄SX₅X₆TX₇YX₈QMNSLRAEDTAVYYC,wherein X₁ is F or V; X₂ is I or L; X₃ is selected from the groupconsisting of L, R, and V; X₄ is K or N; X₅ is selected from the groupconsisting of K, N, R, and S; X₆ is N or S; X₇ is selected from thegroup consisting of A, L, and V; and X₈ is L or M (SEQ ID NO: 229); andFR-H4 comprises WGQGTLVTVSS (SEQ ID NO: 200).
 18. The method of claim17, wherein the heavy chain comprises the following framework sequences:FR-H1 comprises EVQLVESGGGLVQPGGSLRLSCAAS (SEQ ID NO: 197); FR-H2comprises WVRQAPGKGLEWV (SEQ ID NO: 198); FR-H3 comprisesRFTISRDX₁SKNTX₂YLQMNSLRAEDTAVYYCAR, wherein X₁ is N or K; and X₂ isselected from the group consisting of A, L, and V (SEQ ID NO: 230); andFR-H4 comprises WGQGTLVTVSS (SEQ ID NO: 200).
 19. The method of claim14, wherein the light chain comprises the following framework sequences:FR-L1 comprises DIQMTQSPSSLSASVGDRVTITC (SEQ ID NO: 201), FR-L2comprises WYQQKPGKAPKLLIY (SEQ ID NO: 202), FR-L3 comprisesGVPSRFSGSGSGTDFTLTISSLQPEDFATYYC (SEQ ID NO: 203), FR-L4 comprisesFGQGTKVEIK (SEQ ID NO: 221) or FGQGTKVEIKR (SEQ ID NO: 204).
 20. Themethod of claim 14, wherein the light chain comprises the variabledomain sequence of 18F7.v6 as shown in FIG. 27 (SEQ ID NO: 193) or thevariable domain sequence of 18F7.v6k as shown in FIG. 27 (SEQ ID NO:194).
 21. The method of claim 14, wherein the heavy chain comprises thevariable domain sequence of 18F7.v6 as shown in FIG. 28 (SEQ ID NO: 195)or the variable domain sequence of 18F7.v6k as shown in FIG. 28 (SEQ IDNO: 196).
 22. The method of claim 14, wherein the light chain comprisesthe variable domain sequence of 18F7.v6 as shown in FIG. 27 (SEQ ID NO:193) and the heavy chain comprises the variable domain sequence of18F7.v6 as shown in FIG. 28 (SEQ ID NO: 195).
 23. The method of claim14, wherein the light chain comprises the variable domain sequence of18F7.v6k as shown in FIG. 27 (SEQ ID NO: 194) and the heavy chaincomprises the variable domain sequence of 18F7.v6k as shown in FIG. 28(SEQ ID NO: 196).
 24. The method of claim 14, wherein at least a portionof the framework sequence is a human consensus framework sequence. 25.The method of claim 24, comprising human κ subgroup 1 consensusframework sequence or heavy chain human subgroup III consensus frameworksequence.
 26. The method of claim 1 or 14, wherein the pathologicalcondition associated with angiogenesis is a neoplastic condition. 27.The method of claim 26, wherein the neoplastic condition is selectedfrom the group consisting of breast cancer, colorectal cancer, lungcancer, esophageal cancer, bladder cancer, ovarian cancer, pancreaticcancer, and hepatocellular carcinoma.
 28. The method of claim 27,wherein the neoplastic condition is colorectal cancer or lung cancer.29. The method of claim 1 or 14, wherein the pathological conditionassociated with angiogenesis in a non-neoplastic condition.
 30. Themethod of claim 29, wherein said non-neoplastic condition is selectedfrom the group consisting of diabetic and other proliferativeretinopathies, retinopathy of prematurity, neovascular glaucoma,age-related macular degeneration, diabetic macular edema, cornealneovascularization, corneal graft neovascularization, andretinal/choroidal neovascularization.
 31. The method of claim 1 or 14,wherein said anti-angiogenesis agent is an anti-VEGF agent.
 32. Themethod of claim 31, wherein said anti-VEGF agent is an anti-VEGFantibody.
 33. The method of claim 32, wherein said anti-VEGF antibody isbevacizumab or ranibizumab.
 34. The method of claim 1 or 14, furthercomprising administering to the individual an effective amount of afurther medicament.
 35. The method of claim 34, wherein the furthermedicament is a chemotherapeutic agent.
 36. The method of claim 35,wherein the chemotherapeutic agent is FOLFOX.
 37. The method of claim35, wherein the chemotherapeutic agent is carboplatin and paclitaxel.